Substituted nucleotide analogs

ABSTRACT

Disclosed herein are phosphorothioate nucleotide analogs, methods of synthesizing phosphorothioate nucleotide analogs and methods of treating diseases and/or conditions such as viral infections, cancer, and/or parasitic diseases with the phosphorothioate nucleotide analogs.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No. 13/236,435, filed Sep. 19, 2011, which claims the benefit of U.S. Provisional Application Nos. 61/385,363, filed Sep. 22, 2010; and 61/426,461, filed Dec. 22, 2010; all of which are incorporated herein by reference in their entirety, including any drawings.

BACKGROUND

1. Field

The present application relates to the fields of chemistry, biochemistry and medicine. More particularly, disclosed herein are phosphorothioate nucleotide analogs, pharmaceutical compositions that include one or more nucleotide analogs and methods of synthesizing the same. Also disclosed herein are methods of treating diseases and/or conditions with a phosphorothioate nucleotide analog, alone or in combination therapy with other agents.

2. Description

Nucleoside analogs are a class of compounds that have been shown to exert antiviral and anticancer activity both in vitro and in vivo, and thus, have been the subject of widespread research for the treatment of viral infections and cancer. Nucleoside analogs are usually therapeutically inactive compounds that are converted by host or viral enzymes to their respective active anti-metabolites, which, in turn, may inhibit polymerases involved in viral or cell proliferation. The activation occurs by a variety of mechanisms, such as the addition of one or more phosphate groups and, or in combination with, other metabolic processes.

SUMMARY

Some embodiments disclosed herein relate to a compound of Formula (I) or a pharmaceutically acceptable salt thereof.

Some embodiments disclosed herein relate to methods of ameliorating and/or treating a neoplastic disease that can include administering to a subject suffering from the neoplastic disease a therapeutically effective amount of one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof. Other embodiments described herein relate to using one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof, in the manufacture of a medicament for ameliorating and/or treating a neoplastic disease. Still other embodiments described herein relate to one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof, that can be used for ameliorating and/or treating a neoplastic disease.

Some embodiments disclosed herein relate to methods of inhibiting the growth of a tumor that can include administering to a subject having a tumor a therapeutically effective amount of one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof. Other embodiments described herein relate to using one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof, in the manufacture of a medicament for inhibiting the growth of a tumor. Still other embodiments described herein relate to one or more compounds of Formula (I), or a pharmaceutically acceptable salt of thereof, that can be used for inhibiting the growth of a tumor.

Some embodiments disclosed herein relate to methods of ameliorating and/or treating a viral infection that can include administering to a subject suffering from the viral infection a therapeutically effective amount of one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof. Other embodiments described herein relate to using one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof, in the manufacture of a medicament for ameliorating and/or treating a viral infection. Still other embodiments described herein relate to one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof, that can be used for ameliorating and/or treating a viral infection.

Some embodiments disclosed herein relate to methods of ameliorating and/or treating a viral infection that can include contacting a cell infected with the virus with an effective amount of one or more compounds described herein, or a pharmaceutically acceptable salt of one or more compounds described herein, or a pharmaceutical composition that includes one or more compounds described herein, or a pharmaceutically acceptable salt thereof. Other embodiments described herein relate to using one or more compounds described herein, or a pharmaceutically acceptable salt of one or more compounds described herein, in the manufacture of a medicament for ameliorating and/or treating a viral infection that can include contacting a cell infected with the virus with an effective amount of said compound(s). Still other embodiments described herein relate to one or more compounds described herein, or a pharmaceutically acceptable salt of one or more compounds described herein, that can be used for ameliorating and/or treating a viral infection by contacting a cell infected with the virus with an effective amount of said compound(s).

Some embodiments disclosed herein relate to methods of inhibiting replication of a virus that can include contacting a cell infected with the virus with an effective amount of one or more compounds described herein, or a pharmaceutically acceptable salt of one or more compounds described herein, or a pharmaceutical composition that includes one or more compounds described herein, or a pharmaceutically acceptable salt thereof. Other embodiments described herein relate to using one or more compounds described herein, or a pharmaceutically acceptable salt of one or more compounds described herein, in the manufacture of a medicament for inhibiting replication of a virus that can include contacting a cell infected with the virus with an effective amount of said compound(s). Still other embodiments described herein relate to one or more compounds described herein, or a pharmaceutically acceptable salt of one or more compounds described herein, that can be used for inhibiting replication of a virus by contacting a cell infected with the virus with an effective amount of said compound(s).

Some embodiments disclosed herein relate to methods of ameliorating and/or treating a parasitic disease that can include administering to a subject suffering from the parasitic disease a therapeutically effective amount of one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof. Other embodiments described herein relate to using one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof, in the manufacture of a medicament for ameliorating and/or treating a parasitic disease. Still other embodiments described herein relate to one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof, that can be used for ameliorating and/or treating a parasitic disease.

Some embodiments disclosed herein relate to methods of ameliorating and/or treating a viral infection that can include administering to a subject suffering from the viral infection a therapeutically effective amount of a compound described herein or a pharmaceutically acceptable salt thereof (for example, one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof), or a pharmaceutical composition that includes a compound described herein, in combination with an agent selected from an interferon, ribavirin, a HCV protease inhibitor, a HCV polymerase inhibitor, a NS5A inhibitor, an other antiviral compound, a compound of Formula (AA), a mono-, di- and/or tri-phosphate thereof, or a pharmaceutically acceptable salt of the foregoing, a compound of Formula (BB), or a pharmaceutically acceptable salt thereof, and a compound of Formula (DD), or a pharmaceutically acceptable salt thereof. Some embodiments disclosed herein relate to methods of ameliorating and/or treating a viral infection that can include contacting a cell infected with the viral infection with a therapeutically effective amount of a compound described herein or a pharmaceutically acceptable salt thereof (for example, one or more compounds of Formula (I), or a pharmaceutically acceptable salt thereof), or a pharmaceutical composition that includes a compound described herein, in combination with an agent selected from an interferon, ribavirin, a HCV protease inhibitor, a HCV polymerase inhibitor, a NS5A inhibitor, an other antiviral compound, a compound of Formula (AA), a mono-, di- and/or tri-phosphate thereof, or a pharmaceutically acceptable salt of the foregoing, a compound of Formula (BB), or a pharmaceutically acceptable salt thereof, and a compound of Formula (DD), or a pharmaceutically acceptable salt thereof. Some embodiments disclosed herein relate to methods of inhibiting replication of a virus that can include administering to a subject a therapeutically effective amount of a compound described herein or a pharmaceutically acceptable salt thereof (for example, a compound of Formula (I), or a pharmaceutically acceptable salt thereof), or a pharmaceutical composition that includes a compound described herein, or a pharmaceutically acceptable salt thereof, in combination with an agent selected from an interferon, ribavirin, a HCV protease inhibitor, a HCV polymerase inhibitor, a NS5A inhibitor, an other antiviral compound, a compound of Formula (AA), a mono-, di- and/or tri-phosphate thereof, or a pharmaceutically acceptable salt of the foregoing, a compound of Formula (BB), or a pharmaceutically acceptable salt thereof, and a compound of Formula (DD), or a pharmaceutically acceptable salt thereof. In some embodiments, the agent can be a compound, or a pharmaceutically acceptable salt thereof, selected from Compound 1001-1014, 2001-2010, 3001-3008, 4001-4005, 5001-5002, 7000-7077, 8000-8012 or 9000, or a pharmaceutical composition that includes one or more of the aforementioned compounds, or pharmaceutically acceptable salt thereof. In some embodiments, the method can include administering a second agent selected from an interferon, ribavirin, a HCV protease inhibitor, a HCV polymerase inhibitor, a NS5A inhibitor, an other antiviral compound, a compound of Formula (AA), a mono-, di- and/or tri-phosphate thereof, or a pharmaceutically acceptable salt of the foregoing, a compound of Formula (BB), or a pharmaceutically acceptable salt thereof and a compound of Formula (DD), or a pharmaceutically acceptable salt thereof. In some embodiments, the viral infection is HCV.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 illustrates four chromatograms, labeled A, B, C and D, from the results of a hepatocyte activation assay.

FIGS. 2A-2B shows example HCV protease inhibitors.

FIG. 3 shows example nucleoside HCV polymerase inhibitors.

FIG. 4 shows example non-nucleoside HCV polymerase inhibitors.

FIG. 5 shows example NS5A inhibitors.

FIG. 6 shows example other antivirals.

FIGS. 7A-7M show example compounds of Formula (I).

FIGS. 8A-8O show example compounds of Formula (AA), and triphosphates thereof.

FIGS. 9A-9B show example compounds of Formula (BB).

FIG. 10 shows Formula (DD).

DETAILED DESCRIPTION

Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of ordinary skill in the art. All patents, applications, published applications and other publications referenced herein are incorporated by reference in their entirety unless stated otherwise. In the event that there are a plurality of definitions for a term herein, those in this section prevail unless stated otherwise.

As used herein, any “R” group(s) such as, without limitation, R, R¹, R², R^(3a), R^(3b), R⁴, R⁵, R⁶, R⁷, R⁸, R⁹, R¹⁰, R¹¹, R¹², R¹³, R¹⁴, R¹⁵, R¹⁶, R¹⁷, R¹⁸, R¹⁹, R²⁰, R²¹, R^(1A), R^(2A), R^(3A), R^(3B), R^(4A), R^(5A), R^(6A), R^(7A), R^(8A), R^(9A) and R″ represent substituents that can be attached to the indicated atom. An R group may be substituted or unsubstituted. If two “R” groups are described as being “taken together” the R groups and the atoms they are attached to can form a cycloalkyl, aryl, heteroaryl or heterocycle. For example, without limitation, if R^(1a) and R^(1b) of an NR^(1a)R^(1b) group are indicated to be “taken together,” it means that they are covalently bonded to one another to form a ring:

Whenever a group is described as being “optionally substituted” that group may be unsubstituted or substituted with one or more of the indicated substituents. Likewise, when a group is described as being “unsubstituted or substituted” if substituted, the substituent(s) may be selected from one or more the indicated substituents. If no substituents are indicated, it is meant that the indicated “optionally substituted” or “substituted” group may be substituted with one or more group(s) individually and independently selected from alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, heteroaralkyl, (heteroalicyclyl)alkyl, hydroxy, protected hydroxyl, alkoxy, aryloxy, acyl, mercapto, alkylthio, arylthio, cyano, halogen, thiocarbonyl, O-carbamyl, N-carbamyl, O-thiocarbamyl, N-thiocarbamyl, C-amido, N-amido, S-sulfonamido, N-sulfonamido, C-carboxy, protected C-carboxy, O-carboxy, isocyanato, thiocyanato, isothiocyanato, nitro, silyl, sulfenyl, sulfinyl, sulfonyl, haloalkyl, haloalkoxy, trihalomethanesulfonyl, trihalomethanesulfonamido, an amino, a mono-substituted amino group and a di-substituted amino group, and protected derivatives thereof.

As used herein, “C_(a) to C_(b)” in which “a” and “b” are integers refer to the number of carbon atoms in an alkyl, alkenyl or alkynyl group, or the number of carbon atoms in the ring of a cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl or heteroalicyclyl group. That is, the alkyl, alkenyl, alkynyl, ring of the cycloalkyl, ring of the cycloalkenyl, ring of the cycloalkynyl, ring of the aryl, ring of the heteroaryl or ring of the heteroalicyclyl can contain from “a” to “b”, inclusive, carbon atoms. Thus, for example, a “C₁ to C₄ alkyl” group refers to all alkyl groups having from 1 to 4 carbons, that is, CH₃—, CH₃CH₂—, CH₃CH₂CH₂—, (CH₃)₂CH—, CH₃CH₂CH₂CH₂—, CH₃CH₂CH(CH₃)— and (CH₃)₃C—. If no “a” and “b” are designated with regard to an alkyl, alkenyl, alkynyl, cycloalkyl cycloalkenyl, cycloalkynyl, aryl, heteroaryl or heteroalicyclyl group, the broadest range described in these definitions is to be assumed.

As used herein, “alkyl” refers to a straight or branched hydrocarbon chain that comprises a fully saturated (no double or triple bonds) hydrocarbon group. The alkyl group may have 1 to 20 carbon atoms (whenever it appears herein, a numerical range such as “1 to 20” refers to each integer in the given range; e.g., “1 to 20 carbon atoms” means that the alkyl group may consist of 1 carbon atom, 2 carbon atoms, 3 carbon atoms, etc., up to and including 20 carbon atoms, although the present definition also covers the occurrence of the term “alkyl” where no numerical range is designated). The alkyl group may also be a medium size alkyl having 1 to 10 carbon atoms. The alkyl group could also be a lower alkyl having 1 to 6 carbon atoms. The alkyl group of the compounds may be designated as “C₁-C₄ alkyl” or similar designations. By way of example only, “C₁-C₄ alkyl” indicates that there are one to four carbon atoms in the alkyl chain, i.e., the alkyl chain is selected from methyl, ethyl, propyl, iso-propyl, n-butyl, iso-butyl, sec-butyl, and t-butyl. Typical alkyl groups include, but are in no way limited to, methyl, ethyl, propyl, isopropyl, butyl, isobutyl, tertiary butyl, pentyl and hexyl. The alkyl group may be substituted or unsubstituted.

As used herein, “alkenyl” refers to an alkyl group that contains in the straight or branched hydrocarbon chain one or more double bonds. An alkenyl group may be unsubstituted or substituted.

As used herein, “alkynyl” refers to an alkyl group that contains in the straight or branched hydrocarbon chain one or more triple bonds. An alkynyl group may be unsubstituted or substituted.

As used herein, “cycloalkyl” refers to a completely saturated (no double or triple bonds) mono- or multi-cyclic hydrocarbon ring system. When composed of two or more rings, the rings may be joined together in a fused fashion. Cycloalkyl groups can contain 3 to 10 atoms in the ring(s) or 3 to 8 atoms in the ring(s). A cycloalkyl group may be unsubstituted or substituted. Typical cycloalkyl groups include, but are in no way limited to, cyclopropyl, cyclobutyl, cyclopentyl, cyclohexyl, cycloheptyl and cyclooctyl.

As used herein, “cycloalkenyl” refers to a mono- or multi-cyclic hydrocarbon ring system that contains one or more double bonds in at least one ring; although, if there is more than one, the double bonds cannot form a fully delocalized pi-electron system throughout all the rings (otherwise the group would be “aryl,” as defined herein). When composed of two or more rings, the rings may be connected together in a fused fashion. A cycloalkenyl group may be unsubstituted or substituted.

As used herein, “cycloalkynyl” refers to a mono- or multi-cyclic hydrocarbon ring system that contains one or more triple bonds in at least one ring. If there is more than one triple bond, the triple bonds cannot form a fully delocalized pi-electron system throughout all the rings. When composed of two or more rings, the rings may be joined together in a fused fashion. A cycloalkynyl group may be unsubstituted or substituted.

As used herein, “aryl” refers to a carbocyclic (all carbon) monocyclic or multicyclic aromatic ring system (including fused ring systems where two carbocyclic rings share a chemical bond) that has a fully delocalized pi-electron system throughout all the rings. The number of carbon atoms in an aryl group can vary. For example, the aryl group can be a C₆-C₁₄ aryl group, a C₆-C₁₀ aryl group, or a C₆ aryl group. Examples of aryl groups include, but are not limited to, benzene, naphthalene and azulene. An aryl group may be substituted or unsubstituted.

As used herein, “heteroaryl” refers to a monocyclic or multicyclic aromatic ring system (a ring system with fully delocalized pi-electron system) that contain(s) one or more heteroatoms, that is, an element other than carbon, including but not limited to, nitrogen, oxygen and sulfur. The number of atoms in the ring(s) of a heteroaryl group can vary. For example, the heteroaryl group can contain 4 to 14 atoms in the ring(s), 5 to 10 atoms in the ring(s) or 5 to 6 atoms in the ring(s). Furthermore, the term “heteroaryl” includes fused ring systems where two rings, such as at least one aryl ring and at least one heteroaryl ring, or at least two heteroaryl rings, share at least one chemical bond. Examples of heteroaryl rings include, but are not limited to, furan, furazan, thiophene, benzothiophene, phthalazine, pyrrole, oxazole, benzoxazole, 1,2,3-oxadiazole, 1,2,4-oxadiazole, thiazole, 1,2,3-thiadiazole, 1,2,4-thiadiazole, benzothiazole, imidazole, benzimidazole, indole, indazole, pyrazole, benzopyrazole, isoxazole, benzoisoxazole, isothiazole, triazole, benzotriazole, thiadiazole, tetrazole, pyridine, pyridazine, pyrimidine, pyrazine, purine, pteridine, quinoline, isoquinoline, quinazoline, quinoxaline, cinnoline, and triazine. A heteroaryl group may be substituted or unsubstituted.

As used herein, “heterocyclyl” or “heteroalicyclyl” refers to three-, four-, five-, six-, seven-, eight-, nine-, ten-, up to 18-membered monocyclic, bicyclic, and tricyclic ring system wherein carbon atoms together with from 1 to 5 heteroatoms constitute said ring system. A heterocycle may optionally contain one or more unsaturated bonds situated in such a way, however, that a fully delocalized pi-electron system does not occur throughout all the rings. The heteroatom(s) is an element other than carbon including, but not limited to, oxygen, sulfur, and nitrogen. A heterocycle may further contain one or more carbonyl or thiocarbonyl functionalities, so as to make the definition include oxo-systems and thio-systems such as lactams, lactones, cyclic imides, cyclic thioimides and cyclic carbamates. When composed of two or more rings, the rings may be joined together in a fused fashion. Additionally, any nitrogens in a heteroalicyclic may be quaternized. Heterocyclyl or heteroalicyclic groups may be unsubstituted or substituted. Examples of such “heterocyclyl” or “heteroalicyclyl” groups include but are not limited to, 1,3-dioxin, 1,3-dioxane, 1,4-dioxane, 1,2-dioxolane, 1,3-dioxolane, 1,4-dioxolane, 1,3-oxathiane, 1,4-oxathiin, 1,3-oxathiolane, 1,3-dithiole, 1,3-dithiolane, 1,4-oxathiane, tetrahydro-1,4-thiazine, 2H-1,2-oxazine, maleimide, succinimide, barbituric acid, thiobarbituric acid, dioxopiperazine, hydantoin, dihydrouracil, trioxane, hexahydro-1,3,5-triazine, imidazoline, imidazolidine, isoxazoline, isoxazolidine, oxazoline, oxazolidine, oxazolidinone, thiazoline, thiazolidine, morpholine, oxirane, piperidine N-Oxide, piperidine, piperazine, pyrrolidine, pyrrolidone, pyrrolidione, 4-piperidone, pyrazoline, pyrazolidine, 2-oxopyrrolidine, tetrahydropyran, 4H-pyran, tetrahydrothiopyran, thiamorpholine, thiamorpholine sulfoxide, thiamorpholine sulfone, and their benzo-fused analogs (e.g., benzimidazolidinone, tetrahydroquinoline, 3,4-methylenedioxyphenyl).

As used herein, “aralkyl” and “aryl(alkyl)” refer to an aryl group connected, as a substituent, via a lower alkylene group. The lower alkylene and aryl group of an aralkyl may be substituted or unsubstituted. Examples include but are not limited to benzyl, 2-phenylalkyl, 3-phenylalkyl, and naphthylalkyl.

As used herein, “heteroaralkyl” and “heteroaryl(alkyl)” refer to a heteroaryl group connected, as a substituent, via a lower alkylene group. The lower alkylene and heteroaryl group of heteroaralkyl may be substituted or unsubstituted. Examples include but are not limited to 2-thienylalkyl, 3-thienylalkyl, furylalkyl, thienylalkyl, pyrrolylalkyl, pyridylalkyl, isoxazolylalkyl, and imidazolylalkyl, and their benzo-fused analogs.

A “(heteroalicyclyl)alkyl” and “(heterocyclyl)alkyl” refer to a heterocyclic or a heteroalicyclylic group connected, as a substituent, via a lower alkylene group. The lower alkylene and heterocyclyl of a (heteroalicyclyl)alkyl may be substituted or unsubstituted. Examples include but are not limited tetrahydro-2H-pyran-4-yl)methyl, (piperidin-4-yl)ethyl, (piperidin-4-yl)propyl, (tetrahydro-2H-thiopyran-4-yl)methyl, and (1,3-thiazinan-4-yl)methyl.

“Lower alkylene groups” are straight-chained —CH₂— tethering groups, forming bonds to connect molecular fragments via their terminal carbon atoms. Examples include but are not limited to methylene (—CH₂—), ethylene (—CH₂CH₂—), propylene (—CH₂CH₂CH₂—), and butylene (—CH₂CH₂CH₂CH₂—). A lower alkylene group can be substituted by replacing one or more hydrogen of the lower alkylene group with a substituent(s) listed under the definition of “substituted.”

As used herein, “alkoxy” refers to the formula —OR wherein R is an alkyl, an alkenyl, an alkynyl, a cycloalkyl, a cycloalkenyl or a cycloalkynyl is defined as above. A non-limiting list of alkoxys are methoxy, ethoxy, n-propoxy, 1-methylethoxy (isopropoxy), n-butoxy, iso-butoxy, sec-butoxy and tert-butoxy. An alkoxy may be substituted or unsubstituted.

As used herein, “acyl” refers to a hydrogen, alkyl, alkenyl, alkynyl, or aryl connected, as substituents, via a carbonyl group. Examples include formyl, acetyl, propanoyl, benzoyl, and acryl. An acyl may be substituted or unsubstituted.

As used herein, “hydroxyalkyl” refers to an alkyl group in which one or more of the hydrogen atoms are replaced by a hydroxy group. Exemplary hydroxyalkyl groups include but are not limited to, 2-hydroxyethyl, 3-hydroxypropyl, 2-hydroxypropyl, and 2,2-dihydroxyethyl. A hydroxyalkyl may be substituted or unsubstituted.

As used herein, “haloalkyl” refers to an alkyl group in which one or more of the hydrogen atoms are replaced by a halogen (e.g., mono-haloalkyl, di-haloalkyl and tri-haloalkyl). Such groups include but are not limited to, chloromethyl, fluoromethyl, difluoromethyl, trifluoromethyl and 1-chloro-2-fluoromethyl, 2-fluoroisobutyl. A haloalkyl may be substituted or unsubstituted.

As used herein, “haloalkoxy” refers to an alkoxy group in which one or more of the hydrogen atoms are replaced by a halogen (e.g., mono-haloalkoxy, di-haloalkoxy and tri-haloalkoxy). Such groups include but are not limited to, chloromethoxy, fluoromethoxy, difluoromethoxy, trifluoromethoxy and 1-chloro-2-fluoromethoxy, 2-fluoroisobutoxy. A haloalkoxy may be substituted or unsubstituted.

As used herein, “aryloxy” and “arylthio” refers to RO— and RS—, in which R is an aryl, such as but not limited to phenyl. Both an aryloxy and arylthio may be substituted or unsubstituted.

A “sulfenyl” group refers to an “—SR” group in which R can be hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, or (heteroalicyclyl)alkyl. A sulfenyl may be substituted or unsubstituted.

A “sulfinyl” group refers to an “—S(═O)—R” group in which R can be the same as defined with respect to sulfenyl. A sulfinyl may be substituted or unsubstituted.

A “sulfonyl” group refers to an “SO₂R” group in which R can be the same as defined with respect to sulfenyl. A sulfonyl may be substituted or unsubstituted.

An “O-carboxy” group refers to a “RC(═O)O—” group in which R can be hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, or (heteroalicyclyl)alkyl, as defined herein. An O-carboxy may be substituted or unsubstituted.

The terms “ester” and “C-carboxy” refer to a “—C(═O)OR” group in which R can be the same as defined with respect to O-carboxy. An ester and C-carboxy may be substituted or unsubstituted.

A “thiocarbonyl” group refers to a “—C(═S)R” group in which R can be the same as defined with respect to O-carboxy. A thiocarbonyl may be substituted or unsubstituted.

A “trihalomethanesulfonyl” group refers to an “X₃CSO₂—” group wherein X is a halogen.

A “trihalomethanesulfonamido” group refers to an “X₃CS(O)₂N(R_(A))—” group wherein X is a halogen and R_(A) hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, or (heteroalicyclyl)alkyl.

The term “amino” as used herein refers to a —NH₂ group.

As used herein, the term “hydroxy” refers to a —OH group.

A “cyano” group refers to a “—CN” group.

The term “azido” as used herein refers to a —N₃ group.

An “isocyanato” group refers to a “—NCO” group.

A “thiocyanato” group refers to a “—CNS” group.

An “isothiocyanato” group refers to an “—NCS” group.

A “mercapto” group refers to an “—SH” group.

A “carbonyl” group refers to a C═O group.

An “S-sulfonamido” group refers to a “—SO₂N(R_(A)R_(B))” group in which R_(A) and R_(B) can be independently hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, or (heteroalicyclyl)alkyl. An S-sulfonamido may be substituted or unsubstituted.

An “N-sulfonamido” group refers to a “RSO₂N(R_(A))—” group in which R and R_(A) can be independently hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, or (heteroalicyclyl)alkyl. An N-sulfonamido may be substituted or unsubstituted.

An “O-carbamyl” group refers to a “—OC(═O)N(R_(A)R_(B))” group in which R_(A) and R_(B) can be independently hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, or (heteroalicyclyl)alkyl. An O-carbamyl may be substituted or unsubstituted.

An “N-carbamyl” group refers to an “ROC(═O)N(R_(A))—” group in which R and R_(A) can be independently hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, or (heteroalicyclyl)alkyl. An N-carbamyl may be substituted or unsubstituted.

An “O-thiocarbamyl” group refers to a “—OC(═S)—N(R_(A)R_(B))” group in which R_(A) and R_(B) can be independently hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, or (heteroalicyclyl)alkyl. An O-thiocarbamyl may be substituted or unsubstituted.

An “N-thiocarbamyl” group refers to an “ROC(═S)N(R_(A))—” group in which R and R_(A) can be independently hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, or (heteroalicyclyl)alkyl. An N-thiocarbamyl may be substituted or unsubstituted.

A “C-amido” group refers to a “—C(═O)N(R_(A)R_(B))” group in which R_(A) and R_(B) can be independently hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, or (heteroalicyclyl)alkyl. A C-amido may be substituted or unsubstituted.

An “N-amido” group refers to a “RC(═O)N(R_(A))—” group in which R and R_(A) can be independently hydrogen, alkyl, alkenyl, alkynyl, cycloalkyl, cycloalkenyl, cycloalkynyl, aryl, heteroaryl, heteroalicyclyl, aralkyl, or (heteroalicyclyl)alkyl. An N-amido may be substituted or unsubstituted.

The term “halogen atom” or “halogen” as used herein, means any one of the radio-stable atoms of column 7 of the Periodic Table of the Elements, such as, fluorine, chlorine, bromine and iodine.

Where the numbers of substituents is not specified (e.g. haloalkyl), there may be one or more substituents present. For example “haloalkyl” may include one or more of the same or different halogens. As another example, “C₁-C₃ alkoxyphenyl” may include one or more of the same or different alkoxy groups containing one, two or three atoms.

As used herein, the abbreviations for any protective groups, amino acids and other compounds, are, unless indicated otherwise, in accord with their common usage, recognized abbreviations, or the IUPAC-IUB Commission on Biochemical Nomenclature (See, Biochem. 11:942-944 (1972)).

The term “nucleoside” is used herein in its ordinary sense as understood by those skilled in the art, and refers to a compound composed of an optionally substituted pentose moiety or modified pentose moiety attached to a heterocyclic base or tautomer thereof via a N-glycosidic bond, such as attached via the 9-position of a purine-base or the 1-position of a pyrimidine-base. Examples include, but are not limited to, a ribonucleoside comprising a ribose moiety and a deoxyribonucleoside comprising a deoxyribose moiety. A modified pentose moiety is a pentose moiety in which an oxygen atom has been replaced with a carbon and/or a carbon has been replaced with a sulfur or an oxygen atom. A “nucleoside” is a monomer that can have a substituted base and/or sugar moiety. Additionally, a nucleoside can be incorporated into larger DNA and/or RNA polymers and oligomers. In some instances, the nucleoside can be a nucleoside analog drug.

As used herein, the term “heterocyclic base” refers to an optionally substituted nitrogen-containing heterocyclyl that can be attached to an optionally substituted pentose moiety or modified pentose moiety. In some embodiments, the heterocyclic base can be selected from an optionally substituted purine-base, an optionally substituted pyrimidine-base and an optionally substituted triazole-base (for example, a 1,2,4-triazole). The term “purine-base” is used herein in its ordinary sense as understood by those skilled in the art, and includes its tautomers. Similarly, the term “pyrimidine-base” is used herein in its ordinary sense as understood by those skilled in the art, and includes its tautomers. A non-limiting list of optionally substituted purine-bases includes purine, adenine, guanine, hypoxanthine, xanthine, alloxanthine, 7-alkylguanine (e.g. 7-methylguanine), theobromine, caffeine, uric acid and isoguanine. Examples of pyrimidine-bases include, but are not limited to, cytosine, thymine, uracil, 5,6-dihydrouracil and 5-alkylcytosine (e.g., 5-methylcytosine). An example of an optionally substituted triazole-base is 1,2,4-triazole-3-carboxamide. Other non-limiting examples of heterocyclic bases include diaminopurine, 8-oxo-N⁶-alkyladenine (e.g., 8-oxo-N⁶-methyladenine), 7-deazaxanthine, 7-deazaguanine, 7-deazaadenine, N⁴,N⁴-ethanocytosin, N⁶,N⁶-ethano-2,6-diaminopurine, 5-halouracil (e.g., 5-fluorouracil and 5-bromouracil), pseudoisocytosine, isocytosine, isoguanine, and other heterocyclic bases described in U.S. Pat. Nos. 5,432,272 and 7,125,855, which are incorporated herein by reference for the limited purpose of disclosing additional heterocyclic bases. In some embodiments, a heterocyclic base can be optionally substituted with an amine or an enol protecting group(s).

The term “—N-linked amino acid” refers to an amino acid that is attached to the indicated moiety via a main-chain amino or mono-substituted amino group. When the amino acid is attached in an —N-linked amino acid, one of the hydrogens that is part of the main-chain amino or mono-substituted amino group is not present and the amino acid is attached via the nitrogen. As used herein, the term “amino acid” refers to any amino acid (both standard and non-standard amino acids), including, but not limited to, α-amino acids, β-amino acids, γ-amino acids and ε-amino acids. Examples of suitable amino acids include, but are not limited to, alanine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, tyrosine, arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine. Additional examples of suitable amino acids include, but are not limited to, ornithine, hypusine, 2-aminoisobutyric acid, dehydroalanine, gamma-aminobutyric acid, citrulline, beta-alanine, alpha-ethyl-glycine, alpha-propyl-glycine and norleucine. N-linked amino acids can be substituted or unsubstituted.

The term “—N-linked amino acid ester derivative” refers to an amino acid in which a main-chain carboxylic acid group has been converted to an ester group. In some embodiments, the ester group has a formula selected from alkyl-O—C(═O)—, cycloalkyl-O—C(═O)—, aryl-O—C(═O)— and aryl(alkyl)-O—C(═O)—. A non-limiting list of ester groups include, methyl-O—C(═O)—, ethyl-O—C(═O)—, n-propyl-O—C(═O)—, isopropyl-O—C(═O)—, n-butyl-O—C(═O)—, isobutyl-O—C(═O)—, tert-butyl-O—C(═O)—, neopentyl-O—C(═O)—, cyclopropyl-O—C(═O)—, cyclobutyl-O—C(═O)—, cyclopentyl-O—C(═O)—, cyclohexyl-O—C(═O)—, phenyl-O—C(═O)—, and benzyl-O—C(═O)—. N-linked amino acid ester derivatives can be substituted or unsubstituted.

The terms “protecting group” and “protecting groups” as used herein refer to any atom or group of atoms that is added to a molecule in order to prevent existing groups in the molecule from undergoing unwanted chemical reactions. Examples of protecting group moieties are described in T. W. Greene and P. G. M. Wuts, Protective Groups in Organic Synthesis, 3. Ed. John Wiley & Sons, 1999, and in J. F. W. McOmie, Protective Groups in Organic Chemistry Plenum Press, 1973, both of which are hereby incorporated by reference for the limited purpose of disclosing suitable protecting groups. The protecting group moiety may be chosen in such a way, that they are stable to certain reaction conditions and readily removed at a convenient stage using methodology known from the art. A non-limiting list of protecting groups include benzyl; substituted benzyl; alkylcarbonyls and alkoxycarbonyls (e.g., t-butoxycarbonyl (BOC), acetyl, or isobutyryl); arylalkylcarbonyls and arylalkoxycarbonyls (e.g., benzyloxycarbonyl); substituted methyl ether (e.g. methoxymethyl ether); substituted ethyl ether; a substituted benzyl ether; tetrahydropyranyl ether; silyls (e.g., trimethylsilyl, triethylsilyl, triisopropylsilyl, t-butyldimethylsilyl, tri-iso-propylsilyloxymethyl, [2-(trimethylsilyl)ethoxy]methyl or t-butyldiphenylsilyl); esters (e.g. benzoate ester); carbonates (e.g. methoxymethylcarbonate); sulfonates (e.g. tosylate or mesylate); acyclic ketal (e.g. dimethyl acetal); cyclic ketals (e.g., 1,3-dioxane, 1,3-dioxolanes, and those described herein); acyclic acetal; cyclic acetal (e.g., those described herein); acyclic hemiacetal; cyclic hemiacetal; cyclic dithioketals (e.g., 1,3-dithiane or 1,3-dithiolane); orthoesters (e.g., those described herein) and triarylmethyl groups (e.g., trityl; monomethoxytrityl (MMTr); 4,4′-dimethoxytrityl (DMTr); 4,4′,4″-trimethoxytrityl (TMTr); and those described herein).

“Leaving group” as used herein refers to any atom or moiety that is capable of being displaced by another atom or moiety in a chemical reaction. More specifically, in some embodiments, “leaving group” refers to the atom or moiety that is displaced in a nucleophilic substitution reaction. In some embodiments, “leaving groups” are any atoms or moieties that are conjugate bases of strong acids. Examples of suitable leaving groups include, but are not limited to, tosylates and halogens. Non-limiting characteristics and examples of leaving groups can be found, for example in Organic Chemistry, 2d ed., Francis Carey (1992), pages 328-331; Introduction to Organic Chemistry, 2d ed., Andrew Streitwieser and Clayton Heathcock (1981), pages 169-171; and Organic Chemistry, 5th ed., John McMurry (2000), pages 398 and 408; all of which are incorporated herein by reference for the limited purpose of disclosing characteristics and examples of leaving groups.

The term “pharmaceutically acceptable salt” refers to a salt of a compound that does not cause significant irritation to an organism to which it is administered and does not abrogate the biological activity and properties of the compound. In some embodiments, the salt is an acid addition salt of the compound. Pharmaceutical salts can be obtained by reacting a compound with inorganic acids such as hydrohalic acid (e.g., hydrochloric acid or hydrobromic acid), sulfuric acid, nitric acid and phosphoric acid. Pharmaceutical salts can also be obtained by reacting a compound with an organic acid such as aliphatic or aromatic carboxylic or sulfonic acids, for example formic, acetic, succinic, lactic, malic, tartaric, citric, ascorbic, nicotinic, methanesulfonic, ethanesulfonic, p-toluensulfonic, salicylic or naphthalenesulfonic acid. Pharmaceutical salts can also be obtained by reacting a compound with a base to form a salt such as an ammonium salt, an alkali metal salt, such as a sodium or a potassium salt, an alkaline earth metal salt, such as a calcium or a magnesium salt, a salt of organic bases such as dicyclohexylamine, N-methyl-D-glucamine, tris(hydroxymethyl)methylamine, C₁-C₇ alkylamine, cyclohexylamine, triethanolamine, ethylenediamine, and salts with amino acids such as arginine and lysine.

Terms and phrases used in this application, and variations thereof, especially in the appended claims, unless otherwise expressly stated, should be construed as open ended as opposed to limiting. As examples of the foregoing, the term ‘including’ should be read to mean ‘including, without limitation,’ ‘including but not limited to,’ or the like; the term ‘comprising’ as used herein is synonymous with ‘including,’ ‘containing,’ or ‘characterized by,’ and is inclusive or open-ended and does not exclude additional, unrecited elements or method steps; the term ‘having’ should be interpreted as ‘having at least;’ the term ‘includes’ should be interpreted as ‘includes but is not limited to;’ the term ‘example’ is used to provide exemplary instances of the item in discussion, not an exhaustive or limiting list thereof; and use of terms like ‘preferably,’ ‘preferred,’ ‘desired,’ or ‘desirable,’ and words of similar meaning should not be understood as implying that certain features are critical, essential, or even important to the structure or function of the invention, but instead as merely intended to highlight alternative or additional features that may or may not be utilized in a particular embodiment of the invention. In addition, the term “comprising” is to be interpreted synonymously with the phrases “having at least” or “including at least”. When used in the context of a process, the term “comprising” means that the process includes at least the recited steps, but may include additional steps. When used in the context of a compound, composition or device, the term “comprising” means that the compound, composition or device includes at least the recited features or components, but may also include additional features or components. Likewise, a group of items linked with the conjunction ‘and’ should not be read as requiring that each and every one of those items be present in the grouping, but rather should be read as ‘and/or’ unless expressly stated otherwise. Similarly, a group of items linked with the conjunction ‘or’ should not be read as requiring mutual exclusivity among that group, but rather should be read as ‘and/or’ unless expressly stated otherwise.

With respect to the use of substantially any plural and/or singular terms herein, those having skill in the art can translate from the plural to the singular and/or from the singular to the plural as is appropriate to the context and/or application. The various singular/plural permutations may be expressly set forth herein for sake of clarity. The indefinite article “a” or “an” does not exclude a plurality. A single processor or other unit may fulfill the functions of several items recited in the claims. The mere fact that certain measures are recited in mutually different dependent claims does not indicate that a combination of these measures cannot be used to advantage. Any reference signs in the claims should not be construed as limiting the scope.

It is understood that, in any compound described herein having one or more chiral centers, if an absolute stereochemistry is not expressly indicated, then each center may independently be of R-configuration or S-configuration or a mixture thereof. Thus, the compounds provided herein may be enantiomerically pure, enantiomerically enriched, racemic mixture, diastereomerically pure, diastereomerically enriched, or a stereoisomeric mixture. In addition it is understood that, in any compound described herein having one or more double bond(s) generating geometrical isomers that can be defined as E or Z, each double bond may independently be E or Z a mixture thereof.

Likewise, it is understood that, in any compound described, all tautomeric forms are also intended to be included. For example all tautomers of a phosphate and a phosphorothioate groups are intended to be included. Examples of tautomers of a phosphorothioate include the following:

Furthermore, all tautomers of heterocyclic bases known in the art are intended to be included, including tautomers of natural and non-natural purine-bases and pyrimidine-bases.

It is to be understood that where compounds disclosed herein have unfilled valencies, then the valencies are to be filled with hydrogens or isotopes thereof, e.g., hydrogen-1 (protium) and hydrogen-2 (deuterium).

It is understood that the compounds described herein can be labeled isotopically. Substitution with isotopes such as deuterium may afford certain therapeutic advantages resulting from greater metabolic stability, such as, for example, increased in vivo half-life or reduced dosage requirements. Each chemical element as represented in a compound structure may include any isotope of said element. For example, in a compound structure a hydrogen atom may be explicitly disclosed or understood to be present in the compound. At any position of the compound that a hydrogen atom may be present, the hydrogen atom can be any isotope of hydrogen, including but not limited to hydrogen-1 (protium) and hydrogen-2 (deuterium). Thus, reference herein to a compound encompasses all potential isotopic forms unless the context clearly dictates otherwise.

It is understood that the methods and combinations described herein include crystalline forms (also known as polymorphs, which include the different crystal packing arrangements of the same elemental composition of a compound), amorphous phases, salts, solvates, and hydrates. In some embodiments, the compounds described herein exist in solvated forms with pharmaceutically acceptable solvents such as water, ethanol, or the like. In other embodiments, the compounds described herein exist in unsolvated form. Solvates contain either stoichiometric or non-stoichiometric amounts of a solvent, and may be formed during the process of crystallization with pharmaceutically acceptable solvents such as water, ethanol, or the like. Hydrates are formed when the solvent is water, or alcoholates are formed when the solvent is alcohol. In addition, the compounds provided herein can exist in unsolvated as well as solvated forms. In general, the solvated forms are considered equivalent to the unsolvated forms for the purposes of the compounds and methods provided herein.

Where a range of values is provided, it is understood that the upper and lower limit, and each intervening value between the upper and lower limit of the range is encompassed within the embodiments.

Some embodiments disclosed herein relate to a compound of Formula (I) or a pharmaceutically acceptable salt thereof:

wherein: B¹ can be an optionally substituted heterocyclic base or an optionally substituted heterocyclic base with a protected amino group; R¹ can be selected from O⁻, OH, an optionally substituted N-linked amino acid and an optionally substituted N-linked amino acid ester derivative; R² can be selected from an optionally substituted aryl, an optionally substituted heteroaryl, an optionally substituted heterocyclyl and

wherein R¹⁹, R²⁰ and R²¹ can be independently absent or hydrogen, and n can be 0 or 1; provided that when R¹ is O⁻ or OH, then R² is

R^(3a) and R^(3b) can be independently selected from hydrogen, deuterium, an optionally substituted C₁₋₆ alkyl, an optionally substituted C₂₋₆ alkenyl, an optionally substituted C₂₋₆ alkynyl, an optionally substituted C₁₋₆ haloalkyl and aryl(C₁₋₆ alkyl); or R^(3a) and R^(3b) can be taken together to form an optionally substituted C₃₋₆ cycloalkyl; R⁴ can be selected from hydrogen, azido, an optionally substituted C₁₋₆ alkyl, an optionally substituted C₂₋₆ alkenyl and an optionally substituted C₂₋₆ alkynyl; R⁵ can be selected from hydrogen, halogen, azido, cyano, an optionally substituted C₁₋₆ alkyl, —OR¹⁰ and —OC(═O)R¹¹; R⁶ can be selected from hydrogen, halogen, azido, cyano, an optionally substituted C₁₋₆ alkyl, —OR¹² and —OC(═O)R¹³; R⁷ can be selected from hydrogen, halogen, azido, cyano, an optionally substituted C₁₋₆ alkyl, —OR¹⁴ and —OC(═O)R′⁵; or R⁶ and R⁷ can be both oxygen atoms and linked together by a carbonyl group; R⁸ can be selected from hydrogen, halogen, azido, cyano, an optionally substituted C₁₋₆ alkyl, —OR¹⁶ and —OC(═O)R′⁷; R⁹ can be selected from hydrogen, azido, cyano, an optionally substituted C₁₋₆ alkyl and —OR¹⁸; R¹⁰, R¹², R¹⁴, R¹⁶ and R¹⁸ can be independently selected from hydrogen and an optionally substituted C₁₋₆ alkyl; and R¹¹, R¹³, R¹⁵ and R¹⁷ can be independently selected from an optionally substituted C₁₋₆ alkyl and an optionally substituted C₃₋₆ cycloalkyl; with the proviso that when R^(3a), R^(3b), R⁴, R⁵, R⁷, R⁸, and R⁹ are all hydrogen, then R⁶ cannot be azido.

With respect to R², in some embodiments, R² can be an optionally substituted heteroaryl. In other embodiments, R² can be an optionally substituted heterocyclyl. In still other embodiments, R² can be an optionally substituted aryl. For example, R² can be an optionally substituted phenyl or an optionally substituted naphthyl. If R² is a substituted phenyl or a substituted naphthyl, the phenyl ring and the naphthyl ring(s) can be substituted one or more times. Suitable substituents that can be present on optionally substituted phenyl and an optionally substituted naphthyl include electron-donating groups and electron-withdrawing groups. In some embodiments, R² can be a para-substituted phenyl. In other embodiment, R² can be an unsubstituted phenyl or an unsubstituted naphthyl. In yet still other embodiments, R² can be

wherein R¹⁹, R²⁰ and R²¹ can be independently absent or hydrogen, and n can be 0 or 1. In some embodiments, n can be 0. In other embodiments, n can be 1. Those skilled in the art understand when n is 0, R² can be an α-thiodiphosphate. Similarly, those skilled in the art understand when n is 1, R² can be an α-thiotriphosphate. In some embodiments, at least one of R¹⁹, R²⁰ and R²¹ can be absent. In other embodiments, at least one of R¹⁹, R²⁰ and R²¹ can be hydrogen. In some embodiments, R²⁰ and R²¹ can be absent. In other embodiments, R²⁰ and R²¹ can be hydrogen. In some embodiments, R¹⁹, R²⁰ and R²¹ can be absent. In some embodiments, R¹⁹, R²⁰ and R²¹ can be hydrogen. Those skilled in the art understand that when any of R¹⁹, R²⁰ and R²¹ are absent the oxygen atom to which R¹⁹, R²⁰ and R²¹ are associated with can have a negative charge. For example, when R²⁰ is absent, the oxygen atom to which R²⁰ is associated with can be O⁻. Depending upon the substituents attached to each phosphorus atoms, one or more the phosphorus atoms can be a chiral center. For example, when n is 1, the alpha-phosphorus (the phosphorus nearest to the pentose ring) can be a chiral center. In some embodiments, the alpha-phosphorus can be a (R)-stereocenter. In other embodiments, the alpha-phosphorus can be a (S)-stereocenter.

In some embodiments, R¹ can be absent. In other embodiments, R¹ can be hydrogen. In still other embodiments, R¹ can be an optionally substituted N-linked α-amino acid. In yet still other embodiments, R¹ can be an optionally substituted N-linked α-amino acid ester derivative. Various amino acids and amino acid ester derivatives can be used, including those described herein. Suitable amino acids include, but are not limited to, alanine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, tyrosine, arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine. Additional suitable amino acids include, but are not limited to, alpha-ethyl-glycine, alpha-propyl-glycine and beta-alanine. Examples of an N-linked amino acid ester derivatives include, but are not limited to, an ester derivatives of any of the following amino acids: alanine, asparagine, aspartate, cysteine, glutamate, glutamine, glycine, proline, serine, tyrosine, arginine, histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan and valine. Additional examples of N-linked amino acid ester derivatives include, but are not limited to, an ester derivative of any of the following amino acids: alpha-ethyl-glycine, alpha-propyl-glycine and beta-alanine.

In an embodiment, R¹ can be an ester derivative of alanine. In an embodiment, R¹ can be selected from alanine methyl ester, alanine ethyl ester, alanine isopropyl ester, alanine cyclohexyl ester, alanine neopentyl ester, valine isopropyl ester and leucine isopropyl ester. In some embodiments, the optionally substituted N-linked amino acid or the optionally substituted N-linked amino acid ester derivative can be in the L-configuration. In other embodiments, the optionally substituted N-linked amino acid or the optionally substituted N-linked amino acid ester derivative can be in the D-configuration.

In some embodiments, when R¹ is an optionally substituted N-linked α-amino acid or an optionally substituted N-linked α-amino acid ester derivative, then R² can be selected from optionally substituted aryl, an optionally substituted heteroaryl and an optionally substituted heterocyclyl. In some embodiments, when R¹ is an optionally substituted N-linked α-amino acid ester derivative, then R² can be an optionally substituted aryl. In other embodiments, when R¹ is an optionally substituted N-linked α-amino acid ester derivative, then R² can be an optionally substituted heteroaryl. In still other embodiments, when R¹ is an optionally substituted N-linked α-amino acid ester derivative, then R² can be an optionally substituted heterocyclyl.

In some embodiments, R¹ can have the structure

wherein R²² can be selected from hydrogen, an optionally substituted C₁₋₆-alkyl, an optionally substituted C₃₋₆ cycloalkyl, an optionally substituted aryl, an optionally substituted aryl(C₁₋₆ alkyl) and an optionally substituted C₁₋₆ haloalkyl; and R²³ can be selected from hydrogen, an optionally substituted C₁₋₆ alkyl, an optionally substituted C₁₋₆ haloalkyl, an optionally substituted C₃₋₆ cycloalkyl, an optionally substituted C₆ aryl, an optionally substituted C₁₀ aryl and an optionally substituted aryl(C₁₋₆ alkyl); and R²⁴ can be hydrogen or an optionally substituted C₁₋₄-alkyl; or R²³ and R²⁴ can be taken together to form an optionally substituted C₃₋₆ cycloalkyl.

When R¹ has the structure shown above, R²³ can be an optionally substituted C₁₋₆-alkyl. Examples of suitable optionally substituted C₁₋₆-alkyls include optionally substituted variants of the following: methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, tert-butyl, pentyl (branched and straight-chained), and hexyl (branched and straight-chained). When R²³ is substituted, R²³ can be substituted with one or more substituents selected from N-amido, mercapto, alkylthio, an optionally substituted aryl, hydroxy, an optionally substituted heteroaryl, O-carboxy, and amino. In some embodiment, R²³ can be an unsubstituted C₁₋₆-alkyl, such as methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, tert-butyl, pentyl (branched and straight-chained), and hexyl (branched and straight-chained). In an embodiment, R²³ can be methyl.

As to R²², in some embodiments, R²² can be an optionally substituted C₁₋₆ alkyl. Examples of optionally substituted C₁₋₆-alkyls include optionally substituted variants of the following: methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, tert-butyl, pentyl (branched and straight-chained), and hexyl (branched and straight-chained). In some embodiments, R²² can be methyl or isopropyl. In some embodiments, R²² can be ethyl or neopentyl. In other embodiments, R²² can be an optionally substituted C₃₋₆ cycloalkyl. Examples of optionally substituted C₃₋₆ cycloalkyl include optionally substituted variants of the following: cyclopropyl, cyclobutyl, cyclopentyl, and cyclohexyl. In an embodiment, R²² can be an optionally substituted cyclohexyl. In still other embodiments, R²² can be an optionally substituted aryl, such as phenyl and naphthyl. In yet still other embodiments, R²² can be an optionally substituted aryl(C₁₋₆ alkyl). In some embodiments, R²² can be an optionally substituted benzyl. In some embodiments, R²² can be an optionally substituted C₁₋₆ haloalkyl, for example, CF₃.

In some embodiments, R²⁴ can be hydrogen. In other embodiments, R²⁴ can be an optionally substituted C₁₋₄-alkyl, such as methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl and tert-butyl. In an embodiment, R²⁴ can be methyl. In some embodiments, R²³ and R²⁴ can be taken together to form an optionally substituted C₃₋₆ cycloalkyl. Examples of optionally substituted C₃₋₆ cycloalkyl include optionally substituted variants of the following: cyclopropyl, cyclobutyl, cyclopentyl, and cyclohexyl. Depending on the groups that are selected for R²³ and R²⁴, the carbon to which R²³ and R²⁴ are attached may be a chiral center. In some embodiment, the carbon to which R²³ and R²⁴ are attached may be a (R)-chiral center. In other embodiments, the carbon to which R²³ and R²⁴ are attached may be a (S)-chiral center.

As example of a suitable

groups include the following:

The substituents attached to the 5′-position of a compound of Formula (I) can vary. In some embodiments, R^(3a) and R^(3b) can be the same. In other embodiments, R^(3a) and R^(3b) can be different. In some embodiments, R^(3a) and R^(3b) can be both hydrogen. In some embodiments, at least one of R^(3a) and R^(3b) can be an optionally substituted C₁₋₆-alkyl; and the other of R^(3a) and R^(3b) can be hydrogen. Examples of suitable optionally substituted C₁₋₆ alkyls include optionally substituted variants of the following: methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, tert-butyl, pentyl (branched and straight-chained), and hexyl (branched and straight-chained). In an embodiment, at least one of R^(3a) and R^(3b) can be methyl, and the other of R^(3a) and R^(3b) can be hydrogen. In other embodiments, at least one of R^(3a) and R^(3b) can be an optionally substituted C₁₋₆-haloalkyl, and the other of R^(3a) and R^(3b) can be hydrogen. One example of a suitable optionally substituted C₁₋₆-haloalkyl is CF₃. In other still embodiments, R^(3a) and R^(3b) can be taken together to form an optionally substituted C₃₋₆ cycloalkyl. When the substituents attached to the 5′-carbon make the 5′-carbon chiral, in some embodiments, the 5′-carbon can be a (R)-stereocenter. In other embodiments, the 5′-carbon can be an (S)-stereocenter.

The substituents attached to the 4′-carbon can vary. In some embodiments, R⁴ can be hydrogen. In other embodiments, R⁴ can be azido. In still other embodiments, R⁴ can be an optionally substituted C₁₋₆ alkyl, such as optionally substituted variants of the following: methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, tert-butyl, pentyl (branched and straight-chained), and hexyl (branched and straight-chained). In some embodiments, R⁴ can be an optionally substituted C₂₋₆ alkenyl. In some embodiments, R⁴ can be an optionally substituted C₂₋₆ alkynyl.

The substituents attached to the 2′-carbon and the 3′-carbon can also vary. In some embodiments, R⁵ can be hydrogen. In other embodiments, R⁵ can be halogen. In still other embodiments, R⁵ can be azido. In yet still other embodiments, R⁵ can be cyano. In some embodiments, R⁵ can be an optionally substituted C₁₋₆ alkyl, such as optionally substituted variants of the following: methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, tert-butyl, pentyl (branched and straight-chained), and hexyl (branched and straight-chained). In other embodiments, R⁵ can be —OR¹⁰, wherein R¹⁰ can be hydrogen. In still other embodiments, R⁵ can be —OR¹⁰, wherein R¹⁰ can be an optionally substituted C₁₋₆ alkyl. In yet still other embodiments, R⁵ can be —OC(═O)R¹¹, wherein R¹¹ can be an optionally substituted C₁₋₆ alkyl or an optionally substituted C₃₋₆ cycloalkyl. Examples of suitable C₁₋₆ alkyls and C₃₋₆ cycloalkyls are described herein.

In some embodiments, R⁶ can be hydrogen. In other embodiments, R⁶ can be halogen. In still other embodiments, R⁶ can be azido. In yet still other embodiments, R⁶ can be cyano. In some embodiments, R⁶ can be an optionally substituted C₁₋₆ alkyl. In other embodiments, R⁶ can be —OR¹², wherein R¹² can be hydrogen. In still other embodiments, R⁶ can be —OR¹², wherein R¹² can be an optionally substituted C₁₋₆ alkyl. A non-limiting list of examples of R⁶ being —OR¹², wherein R¹² can be an optionally substituted C₁₋₆ alkyl are methoxy, ethoxy, n-propoxy, isopropoxy, n-butoxy, isobutoxy and tert-butoxy, pentoxy (straight-chained or branched) and hexoxy (straight-chained or branched). In yet still other embodiments, R⁶ can be —OC(═O)R¹³, wherein R¹³ can be an optionally substituted C₁₋₆ alkyl or an optionally substituted C₃₋₆ cycloalkyl. Examples of suitable optionally substituted C₁₋₆ alkyls include optionally substituted variants of the following: methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, tert-butyl pentyl (branched and straight-chained), and hexyl (branched and straight-chained). Examples of suitable optionally substituted C₃₋₆ cycloalkyls include optionally substituted variants of the following: cyclopropyl, cyclobutyl, cyclopentyl and cyclohexyl.

In some embodiments, R⁷ can be hydrogen. In other embodiments, R⁷ can be halogen. In still other embodiments, R⁷ can be azido. In yet still other embodiments, R⁷ can be cyano. In some embodiments, R⁷ can be an optionally substituted C₁₋₆ alkyl. In other embodiments, R⁷ can be —OR¹⁴. In an embodiment, when R¹⁴ is hydrogen, R⁷ can be a hydroxy group. In still other embodiments, when R¹⁴ is an optionally substituted C₁₋₆ alkyl, R⁷ can be an optionally substituted C₁₋₆ alkoxy. Examples, of R⁷ being —OR¹⁴, wherein R¹⁴ can be an optionally substituted C₁₋₆ alkyl include, but are not limited to, are methoxy, ethoxy, n-propoxy, isopropoxy, n-butoxy, isobutoxy, tert-butoxy, pentoxy (straight-chained or branched) and hexoxy (straight-chained or branched). In yet still other embodiments, R⁷ can be —OC(═O)R¹⁵, wherein R¹⁵ can be an optionally substituted C₁₋₆ alkyl, such as optionally substituted variants of the following: methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, tert-butyl, pentyl (branched and straight-chained), and hexyl (branched and straight-chained). In some embodiments, R⁷ can be —OC(═O)R¹⁵, wherein R¹⁵ can be an optionally substituted C₃₋₆ cycloalkyl

In some embodiments, R⁸ can be hydrogen. In other embodiments, R⁸ can be halogen. In still other embodiments, R⁸ can be azido. In yet still other embodiments, R⁸ can be cyano. In some embodiments, R⁸ can be —OR¹⁶. When R¹⁶ is hydrogen, R⁸ can be hydroxy. Alternatively, when R¹⁶ is an optionally substituted C₁₋₆ alkyl, R⁸ can be an optionally substituted C₁₋₆ alkoxy. Suitable alkoxy groups are described herein. In other embodiments, R⁸ can be an optionally substituted C₁₋₆ alkyl. In still other embodiments, R⁸ can be —OC(═O)R¹⁷ in which R¹⁷ is an optionally substituted C₁₋₆ alkyl. In yet still other embodiments, R⁸ can be —OC(═O)R¹⁷ in which R¹⁷ is an optionally substituted C₃₋₆ cycloalkyl. Examples of suitable C₁₋₆ alkyl and C₃₋₆ cycloalkyl groups are described herein.

In some embodiments, R⁶ and R⁷ can both be hydroxy. In still other embodiments, R⁶ and R⁷ can both be both oxygen atoms and linked together by a carbonyl group, for example, —O—C(═O)—O—. In some embodiments, at least one of R⁷ and R⁸ can be a halogen. In some embodiments, R⁷ and R⁸ can both be a halogen. In other embodiments, R⁷ can be a halogen and R⁸ can be an optionally substituted C₁₋₆ alkyl, such as those described herein. In other embodiments, R⁷ can be hydrogen and R⁸ can be a halogen. In still other embodiments, at least one of R⁶ and R⁷ can be a hydroxy and R⁸ can be an optionally substituted C₁₋₆ alkyl. In yet still other embodiments, R⁶ can be hydroxy, R⁷ can be hydroxy, H or halogen, and R⁸ can be an optionally substituted C₁₋₆ alkyl. In some embodiments, R^(3a), R^(3b), R⁴, R⁵ and R⁹ can be hydrogen in any of the embodiments described in this paragraph. In some embodiments, B¹ can be an optionally substituted adenine, an optionally substituted guanine, and optionally substituted thymine, optionally substituted cytosine, or an optionally substituted uracil in any of the embodiments described in this paragraph.

In some embodiments, R⁹ can be hydrogen. In other embodiments, R⁹ can be azido. In still other embodiments, R⁹ can be cyano. In yet still other embodiments, R⁹ can be an optionally substituted C₁₋₆ alkyl, such as those described herein. In some embodiments, R⁹ can be —OR¹⁸. In some embodiments, when R⁹ is —OR¹⁸, R⁹ can be a hydroxy group. In other embodiments, when R⁹ is —OR¹⁸, R⁹ can be an optionally substituted C₁₋₆ alkoxy. Examples of optionally substituted C₁₋₆ alkoxy include the following: methoxy, ethoxy, n-propoxy, isopropoxy, n-butoxy, isobutoxy, tert-butoxy, pentoxy (branched and straight-chained), and hexoxy (branched and straight-chained).

Various optionally substituted heterocyclic bases can be attached to the pentose ring. In some embodiments, one or more of the amine and/or amino groups may be protected with a suitable protecting group. For example, an amino group may be protected by transforming the amine and/or amino group to an amide or a carbamate. In some embodiments, an optionally substituted heterocyclic base or an optionally substituted heterocyclic base with one or more protected amino groups can have one of the following structures:

wherein: R^(A2) can be selected from hydrogen, halogen and NHR^(J2), wherein R^(J2) can be selected from hydrogen, —C(═O)R^(K2) and —C(═O)OR^(L2); R^(B2) can be halogen or NHR^(W2), wherein R^(W2) is selected from hydrogen, an optionally substituted C₁₋₆ alkyl, an optionally substituted C₂₋₆ alkenyl, an optionally substituted C₃₋₈ cycloalkyl, —C(═O)R^(M2) and —C(═O)OR^(N2); R^(C2) can be hydrogen or NHR^(O2), wherein R^(O2) can be selected from hydrogen, —C(═O)R^(P2) and —C(═O)OR^(Q2); R^(D2) can be selected from hydrogen, halogen, an optionally substituted C₁₋₆ alkyl, an optionally substituted C₂₋₆ alkenyl and an optionally substituted C₂₋₆ alkynyl; R^(E2) can be selected from hydrogen, an optionally substituted C₁₋₆ alkyl, an optionally substituted C₃₋₈ cycloalkyl, —C(═O)R^(R2) and —C(═O)OR^(S2); R^(F2) can be selected from hydrogen, halogen, an optionally substituted C₁₋₆ alkyl, an optionally substituted C₂₋₆ alkenyl and an optionally substituted C₂₋₆ alkynyl; Y² can be N (nitrogen) or CR^(I2), wherein R^(I2) can be selected from hydrogen, halogen, an optionally substituted C₁₋₆-alkyl, an optionally substituted C₂₋₆-alkenyl and an optionally substituted C₂₋₆-alkynyl; R^(O2) can be an optionally substituted C₁₋₆ alkyl; R^(H2) can be hydrogen or NHR^(T2), wherein R^(T2) can be independently selected from hydrogen, —C(═O)R^(U2) and —C(═O)OR^(V2), and R^(K2), R^(L2), R^(M2), R^(N2), R^(P2), R^(Q2)R^(R2), can be independently selected from C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₆ cycloalkyl, C₃₋₆ cycloalkenyl, C₃₋₆ cycloalkynyl, C₆₋₁₀ aryl, heteroaryl, heteroalicyclyl, aryl(C₁₋₆ alkyl), heteroaryl(C₁₋₆ alkyl) and heteroalicyclyl(C₁₋₆ alkyl). In some embodiments, the structures shown above can be modified by replacing one or more hydrogens with substituents selected from the list of substituents provided for the definition of “substituted.” Suitable optionally substituted C₁₋₆ alkyl groups that can be present on an optionally substituted heterocyclic base or an optionally substituted heterocyclic base with one or more protected amino groups are described herein, and include, optionally substituted variants of the following: methyl, ethyl, n-propyl, isopropyl, n-butyl, isobutyl, tert-butyl, pentyl (branched and straight-chained), and hexyl (branched and straight-chained).

In some embodiments, B¹ can be selected from adenine, guanine, thymine, cytosine and uracil. In some embodiments, R^(B2) can be NH₂. In other embodiments, R^(E2) can be hydrogen. In some embodiments, B¹ can be

In other embodiments, B¹ can be

In some embodiments, B¹ can be

In some embodiments, B¹ can be

In still other embodiments, B¹ can be

In yet still other embodiments, B¹ can be

In some embodiments, B¹ can be

In some embodiments, when R² is a substituted or unsubstituted phenyl, then R¹ cannot be

In other embodiments, when R² is a substituted or unsubstituted phenyl, then R¹ cannot be

In still other embodiments, when R² is a substituted or unsubstituted phenyl and R¹ is

then at least one of R⁵ and R⁶ cannot be hydroxy.

In some embodiments, when R¹ is O⁻ or OH, then R² cannot be

In some embodiments, at least one of R^(3a) and R^(3b) cannot be hydrogen. In some embodiments, R⁴ is not azido. In some embodiments, when R⁴ is not azido, then R⁷ and R⁸ are not both halogen. In some embodiments, when R⁴ is azido, then B¹ is not an optionally substituted uracil, optionally substituted uracil with one or more protected amino groups, an optionally substituted cytosine or optionally substituted cytosine with one or more protected amino groups. In some embodiments, R⁶ cannot be azido. In some embodiments, when R¹ is a methyl ester of glycine, alanine, valine, or phenylalanine; R² is p-chlorophenyl or p-nitrophenyl; B¹ is thymine; and R^(3a), R^(3b), R⁴, R⁵, R⁷, R⁸, and R⁹ are all hydrogen; then R⁶ cannot be azido. In some embodiments, at least one of R⁶ and R⁷ cannot be hydroxy. For example, R⁶ cannot be hydroxy, R⁷ cannot be hydroxy, or both of R⁶ and R⁷ cannot be hydroxy.

Some embodiments disclosed herein relate to a compound of Formula (I) or a pharmaceutically acceptable salt thereof, wherein: B¹ can be an optionally substituted heterocyclic base as described in paragraph [0106]; R¹ can be selected from O⁻, OH, an optionally substituted N-linked amino acid and an optionally substituted N-linked amino acid ester derivative; R² can be selected from an optionally substituted aryl and

wherein R¹⁹, R²⁰ and R²¹ can be independently absent or hydrogen, and n can be 0 or 1; provided that when R¹ is O⁻ or OH, then R² is

R^(3a) and R^(3b) can be hydrogen; R⁴ can be hydrogen; R⁵ can be selected from hydrogen, halogen, an optionally substituted C₁₋₆ alkyl and —OR¹⁰; R⁶ can be selected from hydrogen, halogen, optionally substituted C₁₋₆ alkyl, —OR¹² and —OC(═O)R¹³; R⁷ can be selected from hydrogen, halogen, azido, cyano, an optionally substituted C₁₋₆ alkyl, —OR¹⁴ and —OC(═O)R¹⁵; or R⁶ and R⁷ can be both oxygen atoms and linked together by a carbonyl group; R⁸ can be selected from hydrogen, halogen, an optionally substituted C₁₋₆ alkyl and —OR¹⁶; R⁹ can be hydrogen; R¹⁰, R¹², R¹⁴ and R¹⁶ can be independently selected from hydrogen and an optionally substituted C₁₋₆ alkyl; and R¹³ and R¹⁵ can be independently selected from an optionally substituted C₁₋₆ alkyl and an optionally substituted C₃₋₆ cycloalkyl.

Some embodiments disclosed herein relate to a compound of Formula (I) or a pharmaceutically acceptable salt thereof, wherein: B¹ can be an optionally substituted heterocyclic base or an optionally substituted heterocyclic base with a protected amino group selected from

R¹ can be selected from O⁻, OH, an optionally substituted N-linked amino acid and an optionally substituted N-linked amino acid ester derivative; R² can be selected from an optionally substituted aryl and

wherein R¹⁹, R²⁰ and R²¹ can be independently absent or hydrogen, and n can be 0 or 1; provided that when R¹ is O⁻ or OH, then R² is

R^(3a) and R^(3b) can be hydrogen; R⁴ can be hydrogen; R⁵ can be selected from hydrogen, halogen, an optionally substituted C₁₋₆ alkyl and —OR¹⁰; R⁶ can be selected from hydrogen, halogen, optionally substituted C₁₋₆ alkyl, —OR¹² and —OC(═O)R¹³; R⁷ can be selected from hydrogen, halogen, azido, cyano, an optionally substituted C₁₋₆ alkyl, —OR¹⁴ and —OC(═O)R¹⁵; or R⁶ and R⁷ can be both oxygen atoms and linked together by a carbonyl group; R⁸ can be selected from hydrogen, halogen, an optionally substituted C₁₋₆ alkyl and —OR¹⁶; R⁹ can be hydrogen; R¹⁰, R¹², R¹⁴ and R¹⁶ can be independently selected from hydrogen and an optionally substituted C₁₋₆ alkyl; and R¹³ and R¹⁵ can be independently selected from an optionally substituted C₁₋₆ alkyl and an optionally substituted C₃₋₆ cycloalkyl.

In some embodiments, Formula (I) can be a compound of Formula (Iα), wherein: B¹ can be an optionally substituted heterocyclic base or an optionally substituted heterocyclic base with a protected amino group selected from cytosine, uridine, thymidine, guanine and adenine; R¹ can be selected from O⁻, OH, and an optionally substituted N-linked amino acid ester derivative of alanine, valine, or leucine; R² can be selected from an optionally substituted phenyl, an optionally substituted naphthyl, an optionally substituted pyridyl, an optionally substituted quinolyl, and

wherein R¹⁹, R²⁰ and R²¹ independently can be hydrogen or absent, and n can be 0 or 1; provided that when R¹ is O⁻ or OH, then R² is

R^(3a) and R^(3b) can be hydrogen; R⁴ can be hydrogen; R⁵ can be hydrogen; R⁶ can be —OR¹² or —OC(═O)R¹³; R⁷ can be selected from halogen, —OR¹⁴ and —OC(═O)R¹⁵; R⁸ can be an optionally substituted C₁₋₆ alkyl; R⁹ can be hydrogen; R¹² and R¹⁴ can be independently hydrogen or an optionally substituted C₁₋₆ alkyl; and R¹³ and R¹⁵ can be independently an optionally substituted C₁₋₆ alkyl.

Some embodiments relate to a compound of Formula (I) or a pharmaceutically acceptable salt thereof, wherein: B¹ can be an optionally substituted heterocyclic base or an optionally substituted heterocyclic base with a protected amino group; R¹ can be selected from O⁻, OH, an optionally substituted N-linked amino acid and an optionally substituted N-linked amino acid ester derivative; R² can be selected from an optionally substituted aryl, an optionally substituted heteroaryl, an optionally substituted heterocyclyl and

wherein R¹⁹, R²⁰ and R²¹ can be independently absent or hydrogen, and n can be 0 or 1; provided that when R¹ is O⁻ or OH, then R² is

R^(3a) and R^(3b) can be independently selected from hydrogen, an optionally substituted C₁₋₆ alkyl, an optionally substituted C₂₋₆ alkenyl, an optionally substituted C₂₋₆ alkynyl, an optionally substituted C₁₋₆ haloalkyl and aryl(C₁₋₆ alkyl); or R^(3a) and R^(3b) can be taken together to form an optionally substituted C₃₋₆ cycloalkyl; R⁴ can be selected from hydrogen, azido, an optionally substituted C₁₋₆ alkyl, an optionally substituted C₂₋₆ alkenyl and an optionally substituted C₂₋₆ alkynyl; R⁵ can be selected from hydrogen, halogen, azido, cyano, an optionally substituted C₁₋₆ alkyl, —OR¹⁰ and —OC(═O)R¹¹; R⁶ can be selected from hydrogen, halogen, azido, cyano, an optionally substituted C₁₋₆ alkyl, —OR¹² and —OC(═O)R¹³; R⁷ can be selected from hydrogen, halogen, azido, cyano, an optionally substituted C₁₋₆ alkyl, —OR¹⁴ and —OC(═O)R′⁵; or R⁶ and R⁷ can be both oxygen atoms and linked together by a carbonyl group; R⁸ can be selected from hydrogen, halogen, azido, cyano, an optionally substituted C₁₋₆ alkyl, —OR¹⁶ and —OC(═O)R′⁷; R⁹ can be selected from hydrogen, azido, cyano, an optionally substituted C₁₋₆ alkyl and —OR¹⁸; R¹⁰, R¹², R¹⁴, R¹⁶ and R¹⁸ can be independently selected from hydrogen and an optionally substituted C₁₋₆ alkyl; and R¹¹, R¹³, R¹⁵ and R¹⁷ can be independently an optionally substituted C₁₋₆ alkyl and an optionally substituted C₃₋₆ cycloalkyl.

In some embodiments, a compound of Formula (I) can be a single diastereomer. In other embodiments, a compound of Formula (I) can be a mixture of diastereomers. In some embodiments, a compound of Formula (I) can be a 1:1 mixture of two diastereomers. In some embodiments, a compound of Formula (I) can be diasteriometrically enriched (for example, one diastereomer can be present at a concentration of ≧55%, ≧75%, ≧80%, ≧90%, ≧95%, ≧98%, or ≧99% as compared to the total concentration of the other diastereomers).

Some embodiments of R¹ and R² of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, are provided in Table 1. Tables 2-4 provide the structures of the variables bb01-bb12, aa01-aa11 and es01-es14, respectively. For example, the first entry in Table 1 is “bb01,aa01,es01,” corresponds to a compound of Formula (I), wherein R²

and R¹ is

TABLE 1 R², R¹, R_(α) bb01,aa01,es01 bb01,aa01,es02 bb01,aa01,es03 bb01,aa01,es04 bb01,aa01,es05 bb01,aa01,es06 bb01,aa01,es07 bb01,aa01,es08 bb01,aa01,es09 bb01,aa01,es10 bb01,aa01,es11 bb01,aa01,es12 bb01,aa02,es01 bb01,aa02,es02 bb01,aa02,es03 bb01,aa02,es04 bb01,aa02,es05 bb01,aa02,es06 bb01,aa02,es07 bb01,aa02,es08 bb01,aa02,es09 bb01,aa02,es10 bb01,aa02,es11 bb01,aa02,es12 bb01,aa03,es01 bb01,aa03,es02 bb01,aa03,es03 bb01,aa03,es04 bb01,aa03,es05 bb01,aa03,es06 bb01,aa03,es07 bb01,aa03,es08 bb01,aa03,es09 bb01,aa03,es10 bb01,aa03,es11 bb01,aa03,es12 bb01,aa04,es01 bb01,aa04,es02 bb01,aa04,es03 bb01,aa04,es04 bb01,aa04,es05 bb01,aa04,es06 bb01,aa04,es07 bb01,aa04,es08 bb01,aa04,es09 bb01,aa04,es10 bb01,aa04,es11 bb01,aa04,es12 bb01,aa05,es01 bb01,aa05,es02 bb01,aa05,es03 bb01,aa05,es04 bb01,aa05,es05 bb01,aa05,es06 bb01,aa05,es07 bb01,aa05,es08 bb01,aa05,es09 bb01,aa05,es10 bb01,aa05,es11 bb01,aa05,es12 bb01,aa06,es01 bb01,aa06,es02 bb01,aa06,es03 bb01,aa06,es04 bb01,aa06,es05 bb01,aa06,es06 bb01,aa06,es07 bb01,aa06,es08 bb01,aa06,es09 bb01,aa06,es10 bb01,aa06,es11 bb01,aa06,es12 bb01,aa07,es01 bb01,aa07,es02 bb01,aa07,es03 bb01,aa07,es04 bb01,aa07,es05 bb01,aa07,es06 bb01,aa07,es07 bb01,aa07,es08 bb01,aa07,es09 bb01,aa07,es10 bb01,aa07,es11 bb01,aa07,es12 bb01,aa08,es01 bb01,aa08,es02 bb01,aa08,es03 bb01,aa08,es04 bb01,aa08,es05 bb01,aa08,es06 bb01,aa08,es07 bb01,aa08,es08 bb01,aa08,es09 bb01,aa08,es10 bb01,aa08,es11 bb01,aa08,es12 bb01,aa09,es01 bb01,aa09,es02 bb01,aa09,es03 bb01,aa09,es04 bb01,aa09,es05 bb01,aa09,es06 bb01,aa09,es07 bb01,aa09,es08 bb01,aa09,es09 bb01,aa09,es10 bb01,aa09,es11 bb01,aa09,es12 bb01,aa10,es01 bb01,aa10,es02 bb01,aa10,es03 bb01,aa10,es04 bb01,aa10,es05 bb01,aa10,es06 bb01,aa10,es07 bb01,aa10,es08 bb01,aa10,es09 bb01,aa10,es10 bb01,aa10,es11 bb01,aa10,es12 bb02,aa01,es01 bb02,aa01,es02 bb02,aa01,es03 bb02,aa01,es04 bb02,aa01,es05 bb02,aa01,es06 bb02,aa01,es07 bb02,aa01,es08 bb02,aa01,es09 bb02,aa01,es10 bb02,aa01,es11 bb02,aa01,es12 bb02,aa02,es01 bb02,aa02,es02 bb02,aa02,es03 bb02,aa02,es04 bb02,aa02,es05 bb02,aa02,es06 bb02,aa02,es07 bb02,aa02,es08 bb02,aa02,es09 bb02,aa02,es10 bb02,aa02,es11 bb02,aa02,es12 bb02,aa03,es01 bb02,aa03,es02 bb02,aa03,es03 bb02,aa03,es04 bb02,aa03,es05 bb02,aa03,es06 bb02,aa03,es07 bb02,aa03,es08 bb02,aa03,es09 bb02,aa03,es10 bb02,aa03,es11 bb02,aa03,es12 bb02,aa04,es01 bb02,aa04,es02 bb02,aa04,es03 bb02,aa04,es04 bb02,aa04,es05 bb02,aa04,es06 bb02,aa04,es07 bb02,aa04,es08 bb02,aa04,es09 bb02,aa04,es10 bb02,aa04,es11 bb02,aa04,es12 bb02,aa05,es01 bb02,aa05,es02 bb02,aa05,es03 bb02,aa05,es04 bb02,aa05,es05 bb02,aa05,es06 bb02,aa05,es07 bb02,aa05,es08 bb02,aa05,es09 bb02,aa05,es10 bb02,aa05,es11 bb02,aa05,es12 bb02,aa06,es01 bb02,aa06,es02 bb02,aa06,es03 bb02,aa06,es04 bb02,aa06,es05 bb02,aa06,es06 bb02,aa06,es07 bb02,aa06,es08 bb02,aa06,es09 bb02,aa06,es10 bb02,aa06,es11 bb02,aa06,es12 bb02,aa07,es01 bb02,aa07,es02 bb02,aa07,es03 bb02,aa07,es04 bb02,aa07,es05 bb02,aa07,es06 bb02,aa07,es07 bb02,aa07,es08 bb02,aa07,es09 bb02,aa07,es10 bb02,aa07,es11 bb02,aa07,es12 bb02,aa08,es01 bb02,aa08,es02 bb02,aa08,es03 bb02,aa08,es04 bb02,aa08,es05 bb02,aa08,es06 bb02,aa08,es07 bb02,aa08,es08 bb02,aa08,es09 bb02,aa08,es10 bb02,aa08,es11 bb02,aa08,es12 bb02,aa09,es01 bb02,aa09,es02 bb02,aa09,es03 bb02,aa09,es04 bb02,aa09,es05 bb02,aa09,es06 bb02,aa09,es07 bb02,aa09,es08 bb02,aa09,es09 bb02,aa09,es10 bb02,aa09,es11 bb02,aa09,es12 bb02,aa10,es01 bb02,aa10,es02 bb02,aa10,es03 bb02,aa10,es04 bb02,aa10,es05 bb02,aa10,es06 bb02,aa10,es07 bb02,aa10,es08 bb02,aa10,es09 bb02,aa10,es10 bb02,aa10,es11 bb02,aa10,es12 bb03,aa03,es01 bb03,aa03,es02 bb03,aa03,es03 bb03,aa03,es04 bb03,aa03,es05 bb03,aa03,es06 bb03,aa03,es07 bb03,aa03,es08 bb03,aa03,es09 bb03,aa03,es10 bb03,aa03,es11 bb03,aa03,es12 bb03,aa04,es01 bb03,aa04,es02 bb03,aa04,es03 bb03,aa04,es04 bb03,aa04,es05 bb03,aa04,es06 bb03,aa04,es07 bb03,aa04,es08 bb03,aa04,es09 bb03,aa04,es10 bb03,aa04,es11 bb03,aa04,es12 bb03,aa05,es01 bb03,aa05,es02 bb03,aa05,es03 bb03,aa05,es04 bb03,aa05,es05 bb03,aa05,es06 bb03,aa05,es07 bb03,aa05,es08 bb03,aa05,es09 bb03,aa05,es10 bb03,aa05,es11 bb03,aa05,es12 bb03,aa06,es01 bb03,aa06,es02 bb03,aa06,es03 bb03,aa06,es04 bb03,aa06,es05 bb03,aa06,es06 bb03,aa06,es07 bb03,aa06,es08 bb03,aa06,es09 bb03,aa06,es10 bb03,aa06,es11 bb03,aa06,es12 bb03,aa07,es01 bb03,aa07,es02 bb03,aa07,es03 bb03,aa07,es04 bb03,aa07,es05 bb03,aa07,es06 bb03,aa07,es07 bb03,aa07,es08 bb03,aa07,es09 bb03,aa07,es10 bb03,aa07,es11 bb03,aa07,es12 bb03,aa08,es01 bb03,aa08,es02 bb03,aa08,es03 bb03,aa08,es04 bb03,aa08,es05 bb03,aa08,es06 bb03,aa08,es07 bb03,aa08,es08 bb03,aa08,es09 bb03,aa08,es10 bb03,aa08,es11 bb03,aa08,es12 bb03,aa09,es01 bb03,aa09,es02 bb03,aa09,es03 bb03,aa09,es04 bb03,aa09,es05 bb03,aa09,es06 bb03,aa09,es07 bb03,aa09,es08 bb03,aa09,es09 bb03,aa09,es10 bb03,aa09,es11 bb03,aa09,es12 bb03,aa10,es01 bb03,aa10,es02 bb03,aa10,es03 bb03,aa10,es04 bb03,aa10,es05 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bb08,aa09,es12 bb08,aa10,es01 bb08,aa10,es02 bb08,aa10,es03 bb08,aa10,es04 bb08,aa10,es05 bb08,aa10,es06 bb08,aa10,es07 bb08,aa10,es08 bb08,aa10,es09 bb08,aa10,es10 bb08,aa10,es11 bb08,aa10,es12 bb09,aa01,es01 bb09,aa01,es02 bb09,aa01,es03 bb09,aa01,es04 bb09,aa01,es05 bb09,aa01,es06 bb09,aa01,es07 bb09,aa01,es08 bb09,aa01,es09 bb09,aa01,es10 bb09,aa01,es11 bb09,aa01,es12 bb09,aa02,es01 bb09,aa02,es02 bb09,aa02,es03 bb09,aa02,es04 bb09,aa02,es05 bb09,aa02,es06 bb09,aa02,es07 bb09,aa02,es08 bb09,aa02,es09 bb09,aa02,es10 bb09,aa02,es11 bb09,aa02,es12 bb09,aa03,es01 bb09,aa03,es02 bb09,aa03,es03 bb09,aa03,es04 bb09,aa03,es05 bb09,aa03,es06 bb09,aa03,es07 bb09,aa03,es08 bb09,aa03,es09 bb09,aa03,es10 bb09,aa03,es11 bb09,aa03,es12 bb09,aa04,es01 bb09,aa04,es02 bb09,aa04,es03 bb09,aa04,es04 bb09,aa04,es05 bb09,aa04,es06 bb09,aa04,es07 bb09,aa04,es08 bb09,aa04,es09 bb09,aa04,es10 bb09,aa04,es11 bb09,aa04,es12 bb09,aa05,es01 bb09,aa05,es02 bb09,aa05,es03 bb09,aa05,es04 bb09,aa05,es05 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bb09,aa10,es12 bb10,aa01,es01 bb10,aa01,es02 bb10,aa01,es03 bb10,aa01,es04 bb10,aa01,es05 bb10,aa01,es06 bb10,aa01,es07 bb10,aa01,es08 bb10,aa01,es09 bb10,aa01,es10 bb10,aa01,es11 bb10,aa01,es12 bb10,aa02,es01 bb10,aa02,es02 bb10,aa02,es03 bb10,aa02,es04 bb10,aa02,es05 bb10,aa02,es06 bb10,aa02,es07 bb10,aa02,es08 bb10,aa02,es09 bb10,aa02,es10 bb10,aa02,es11 bb10,aa02,es12 bb10,aa03,es01 bb10,aa03,es02 bb10,aa03,es03 bb10,aa03,es04 bb10,aa03,es05 bb10,aa03,es06 bb10,aa03,es07 bb10,aa03,es08 bb10,aa03,es09 bb10,aa03,es10 bb10,aa03,es11 bb10,aa03,es12 bb10,aa04,es01 bb10,aa04,es02 bb10,aa04,es03 bb10,aa04,es04 bb10,aa04,es05 bb10,aa04,es06 bb10,aa04,es07 bb10,aa04,es08 bb10,aa04,es09 bb10,aa04,es10 bb10,aa04,es11 bb10,aa04,es12 bb10,aa05,es01 bb10,aa05,es02 bb10,aa05,es03 bb10,aa05,es04 bb10,aa05,es05 bb10,aa05,es06 bb10,aa05,es07 bb10,aa05,es08 bb10,aa05,es09 bb10,aa05,es10 bb10,aa05,es11 bb10,aa05,es12 bb10,aa06,es01 bb10,aa06,es02 bb10,aa06,es03 bb10,aa06,es04 bb10,aa06,es05 bb10,aa06,es06 bb10,aa06,es07 bb10,aa06,es08 bb10,aa06,es09 bb10,aa06,es10 bb10,aa06,es11 bb10,aa06,es12 bb10,aa07,es01 bb10,aa07,es02 bb10,aa07,es03 bb10,aa07,es04 bb10,aa07,es05 bb10,aa07,es06 bb10,aa07,es07 bb10,aa07,es08 bb10,aa07,es09 bb10,aa07,es10 bb10,aa07,es11 bb10,aa07,es12 bb10,aa08,es01 bb10,aa08,es02 bb10,aa08,es03 bb10,aa08,es04 bb10,aa08,es05 bb10,aa08,es06 bb10,aa08,es07 bb10,aa08,es08 bb10,aa08,es09 bb10,aa08,es10 bb10,aa08,es11 bb10,aa08,es12 bb10,aa09,es01 bb10,aa09,es02 bb10,aa09,es03 bb10,aa09,es04 bb10,aa09,es05 bb10,aa09,es06 bb10,aa09,es07 bb10,aa09,es08 bb10,aa09,es09 bb10,aa09,es10 bb10,aa09,es11 bb10,aa09,es12 bb10,aa10,es01 bb10,aa10,es02 bb10,aa10,es03 bb10,aa10,es04 bb10,aa10,es05 bb10,aa10,es06 bb10,aa10,es07 bb10,aa10,es08 bb10,aa10,es09 bb10,aa10,es10 bb10,aa10,es11 bb10,aa10,es12

TABLE 2

bb01

bb02

bb03

bb04

bb05

bb06

bb07

bb08

bb09

bb10

TABLE 3

aa01

aa02

aa03

aa04

aa05

aa06

aa07

aa08

aa09

aa10

TABLE 4 es01 R_(α) = methyl es02 R_(α) = ethyl es03 R_(α) = isopropyl es04 R_(α) = propyl es05 R_(α) = cyclohexyl es06 R_(α) = cyclopentyl es07 R_(α) = cyclobutyl es08 R_(α) = cyclopropyl es09 R_(α) = benzyl es11 R_(α) = neopentyl es10 R_(α) = t-butyl es12 R_(α) = hydrogen

In some embodiments, R^(3a), R^(3b), R⁴, R⁵ and R⁹ can be all hydrogens in any of the embodiments described in Table 1. In some embodiments, at least one of R⁶ and R⁷ can be OH in any of the embodiments described in Table 1. In some embodiments, R⁸ can be a C₁₋₆ alkyl in any of the embodiments described in Table 1. In some embodiments, B¹ can be adenine, guanine, uracil, thymine or cystine in any of the embodiments described in Table 1. In some embodiments, R^(3a), R^(3b), R⁴, R⁵, R⁶, R⁷, R⁸, R⁹ and B¹ can be the groups provided with respect to Formula (Iα) in any of the embodiments described in Table 1.

Examples of compounds of Formula (I) include, but are not limited to the following:

Additional examples of compounds of Formula (I) include, but are not limited to the following:

In some embodiments, the compound of Formula (I) can be the following:

Additional examples of compounds of Formula (I) include the following:

In some embodiments, neutralizing the charge on the thiophosphate group may facilitate the penetration of the cell membrane by a compound of Formula (I) (including a compound of Formula (Iα)) by making the compound more lipophilic compared to a thionucleotide having a comparable structure with one or more charges present on the phosphate. Once absorbed and taken inside the cell, the groups attached to the thiophosphate can be easily removed by esterases, proteases, or other enzymes. In some embodiments, the groups attached to the thiophosphate can be removed by simple hydrolysis. Inside the cell, the thio-monophosphate thus released may then be metabolized by cellular enzymes to the thio-diphosphate or the active thio-triphosphate. In some embodiments, the phosphorylation of a thio-monophosphate of a compound of Formula (I), or pharmaceutically acceptable salt thereof, can be stereoselective. For example, a thio-monophosphate of a compound of Formula (I) (including a compound of Formula (Iα)) can be phosphorylated to give an alpha-thiodiphosphate and/or an alpha-thiotriphosphate compound that can be enriched in the (R) or (S) diastereomer with respect to the 5′-O-phosphorous atom. For example, one of the (R) and (S) configuration with respect to the 5′-O-phosphorous atom of the alpha-thiodiphosphate and/or the alpha-thiotriphosphate compound can be present in an amount >50%, ≧75%, ≧90%, ≧95% or ≧99% compared to the amount of the other of the (R) or (S) configuration with respect to the 5′-O-phosphorous atom. In some embodiments, phosphorylation of a compound of Formula (I), or pharmaceutically acceptable salt thereof, can result in the formation of a compound that has the (R)-configuration at the 5′-O-phosphorous atom. In some embodiments, phosphorylation of a compound of Formula (I), or pharmaceutically acceptable salt thereof, can result in formation of a compound that has the (S)-configuration at the 5′-O-phosphorous atom.

In some embodiments, a compound of Formula (I) (including a compound of Formula (Iα)), or a pharmaceutically acceptable salt thereof, can act as a chain terminator of HCV replication. For example, incorporation of a compound of Formula (I) containing a moiety at the 2′-carbon position can terminate further elongation of the RNA chain of HCV. For example, a compound of Formula (I) can contain a 2′-carbon modification when R⁸ is a non-hydrogen group selected from halogen, azido, cyano, an optionally substituted C₁₋₆ alkyl, —OR¹⁶ and —OC(═O)R¹⁷.

In some embodiments, a compound of Formula (I) (including a compound of Formula (Iα)), or a pharmaceutically acceptable salt thereof, can have increased metabolic and/or plasma stability. In some embodiments, a compound of Formula (I) (including a compound of Formula (Iα)), or a pharmaceutically acceptable salt thereof, can be more resistant to hydrolysis and/or more resistant to enzymatic transformations. For example, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can have increased metabolic stability, increased plasma stability, can be more resistant to hydrolysis and/or can be more resistant to enzymatic transformations compared to a compound that is identical in structure but for having a phosphate attached to the 5′-carbon of the ribose ring. In some embodiments, a compound of Formula (I) (including a compound of Formula (Iα)), or a pharmaceutically acceptable salt thereof, can have improved properties. In previous studies, replacing a sulfur with an oxygen on the alpha-phosphate of a nucleotide phosphoramidate has resulted in more than a 1000-fold decrease in potency. See Venkatachalam et al. European Journal of Medicinal Chemistry (2004) 39:665-683. A non-limiting list of example properties include, but are not limited to, increased biological half life, increased bioavailability, increase potency, a sustained in vivo response, increased dosing intervals, decreased dosing amounts, decreased cytotoxicity, reduction in required amounts for treating disease conditions, reduction in viral load, reduction in time to seroconversion (i.e., the virus becomes undetectable in patient serum), increased sustained viral response, a reduction of morbidity or mortality in clinical outcomes, increased subject compliance, decreased liver conditions (such as liver fibrosis, liver cirrhosis and/or liver cancer), and compatibility with other medications. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can have a biological half life of greater than 24 hours. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can have a biological half life in the range of about 40 hours to about 46 hours. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can have a biological half life greater than a compound that has a phosphate attached to the 5′-carbon of the ribose ring (for example, a compound that is identical in structure but for having a phosphate attached to the 5′-carbon of the ribose ring). In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can have more potent antiviral activity (for example, a lower IC₅₀ in an HCV replicon assay) as compared to the current standard of care.

Synthesis

Compounds of Formula (I) (including compounds of Formula (Iα)), and those described herein may be prepared in various ways. General synthetic routes to the compound of Formula (I), and some examples of starting materials used to synthesize the compounds of Formula (I) are shown in Scheme 1, and described herein. The routes shown and described herein are illustrative only and are not intended, nor are they to be construed, to limit the scope of the claims in any manner whatsoever. Those skilled in the art will be able to recognize modifications of the disclosed syntheses and to devise alternate routes based on the disclosures herein; all such modifications and alternate routes are within the scope of the claims.

One method for forming a compound of Formula (I) is shown in Scheme 1. In Scheme 1, R^(3A), R^(3B), R^(4A), R^(5A), R^(6A), R^(7A), R^(8A), R^(9A) and B^(1A) can be the same as R^(3a), R^(3b), R⁴, R⁵, R⁶, R⁷, R⁸, R⁹ and B¹ as described herein for Formula (I); and R¹ and R² can be the same as described herein for Formula (I). As shown in Scheme 1, a compound of Formula (A) can be reacted with a compound having the formula R²O—P(═S)(R¹)—Cl to form a compound of Formula (I).

To reduce the formation of side products, one or more the groups attached to the pentose ring can be protected with one or more suitable protecting groups. As an example, if R^(6A) and/or R^(7A) is/are hydroxy group(s), the hydroxy group(s) can be protected with suitable protecting groups, such as triarylmethyl and/or silyl groups. Examples of triarylmethyl groups include but are not limited to, trityl, monomethoxytrityl (MMTr), 4,4′-dimethoxytrityl (DMTr), 4,4′,4″-trimethoxytrityl (TMTr), 4,4′,4″-tris-(benzoyloxy)trityl (TBTr), 4,4′,4″-tris(4,5-dichlorophthalimido)trityl (CPTr), 4,4′,4″-tris(levulinyloxy)trityl (TLTr), p-anisyl-1-naphthylphenylmethyl, di-o-anisyl-1-naphthylmethyl, p-tolyldipheylmethyl, 3-(imidazolylmethyl)-4,4′-dimethoxytrityl, 9-phenylxanthen-9-yl (Pixyl), 9-(p-methoxyphenyl) xanthen-9-yl (Mox), 4-decyloxytrityl, 4-hexadecyloxytrityl, 4,4′-dioctadecyltrityl, 9-(4-octadecyloxyphenyl) xanthen-9-yl, 1,1′-bis-(4-methoxyphenyl)-1′-pyrenylmethyl, 4,4′,4″-tris-(tert-butylphenyl) methyl (TTTr) and 4,4′-di-3,5-hexadienoxytrityl. Examples of suitable silyl groups are described herein. Alternatively, R^(6A) and/or R^(7A) can be protected by a single achiral or chiral protecting group, for example, by forming an orthoester, a cyclic acetal or a cyclic ketal. Suitable orthoesters include methoxymethylene acetal, ethoxymethylene acetal, 2-oxacyclopentylidene orthoester, dimethoxymethylene orthoester, 1-methoxyethylidene orthoester, 1-ethoxyethylidene orthoester, methylidene orthoester, phthalide orthoester 1,2-dimethoxyethylidene orthoester, and alpha-methoxybenzylidene orthoester; suitable cyclic acetals include methylene acetal, ethylidene acetal, t-butylmethylidene acetal, 3-(benzyloxy)propyl acetal, benzylidene acetal, 3,4-dimethoxybenzylidene acetal and p-acetoxybenzylidene acetal; and suitable cyclic ketals include 1-t-butylethylidene ketal, 1-phenylethylidene ketal, isopropylidene ketal, cyclopentylidene ketal, cyclohexylidene ketal, cycloheptylidene ketal and 1-(4-methoxyphenyl)ethylidene ketal.

If desired, any —NH and/or NH₂ groups present on the B^(1A) can also be protected with one or more suitable protecting groups. Examples of suitable protecting groups include triarylmethyl groups and silyl groups. Examples of silyl groups include, but are not limited to, trimethylsilyl (TMS), tert-butyldimethylsilyl (TBDMS), triisopropylsilyl (TIPS), tert-butyldiphenylsilyl (TBDPS), tri-iso-propylsilyloxymethyl and [2-(trimethylsilyl)ethoxy]methyl.

Suitable thiophosphorochloridates can be commercially obtained or prepared by a synthetic method described herein. An example of a general structure of a thiophosphorochloridate is shown in Scheme 1. In some embodiments, the thiophosphorochloridate can be coupled to a compound of Formula (A). In some embodiments, to facilitate the coupling, a Grignard reagent can be used. Suitable Grignard reagents are known to those skilled in the art and include, but are not limited to, alkylmagnesium chlorides and alkylmagnesium bromides. In other embodiments, the thiophosphorochloridate can be added to a compound of Formula (A) using a base. Suitable bases are known to those skilled in the art. Examples of bases include, but are not limited to, an amine base, such as an alkylamine (including mono-, di- and tri-alkylamines (e.g., triethylamine)), optionally substituted pyridines (e.g. collidine) and optionally substituted imidzoles (e.g., N-methylimidazole)).

When at least one of R^(3a) and R^(3b) is an optionally substituted C₁₋₆ alkyl or an optionally substituted C₁₋₆ haloalkyl, the optionally substituted C₁₋₆ alkyl or the optionally substituted C₁₋₆ haloalkyl can be added to the 5′-position using methods known to those skilled in the art. In some embodiments, the hydroxy attached to the 5′-carbon can be oxidized to an aldehyde. Suitable oxidation conditions include, but are not limited to, DMSO in combination with an activating agent (usually an acylating agent or an acid) and an amine base, Moffatt oxidation, Swern oxidation and Corey-Kim oxidation, and suitable oxidizing agents include, but are not limited to, Dess-Martin periodinane, TPAP/NMO (tetrapropylammonium perruthenate/N-methylmorpholine N-oxide), Swern oxidation reagent, PCC (pyridinium chlorochromate), and/or PDC (pyridinium dichromate), sodium periodate, Collin's reagent, ceric ammonium nitrate CAN, Na₂Cr₂O₇ in water, Ag₂CO₃ on celite, hot HNO₃ in aqueous glyme, O₂-pyridine CuCl, Pb(OAc)₄-pyridine and benzoyl peroxide-NiBr₂. The resulting aldehyde compound can be reacted with a Grignard reagent, an organolithium reagent or trialkylaluminum (e.g., trimethylaluminum) to form a compound of Formula (A) where at least one of R^(3A) and R^(3B) is an optionally substituted C₁₋₆ alkyl or an optionally substituted C₁₋₆ haloalkyl. Optionally, the alkylating reagents can be in the presence of a Lewis acid. Suitable Lewis acids are known to those skilled in the art.

The chirality of the 5′-carbon of compounds of Formulae (A) and/or (I) can be inverted using methods known to the skilled in the art. For example, the oxygen attached to the 5′-carbon can be oxidized, for example to an aldehyde, for a compound of Formula (A), or ketone, for a compound of Formula (I), using a suitable oxidizing agent. The aldehyde and/or ketone can then be reduced using a suitable reducing agent. Examples of suitable reducing agents include, but are not limited to, NaH, LiH, NaBH₄, LiAlH₄ and CaH₂. Suitable oxidizing and reducing agents are known to those skilled in the art. Examples of suitable oxidizing agents and conditions are described herein.

As described herein, in some embodiments, R⁶ and R⁷ can be both oxygen atoms linked together by a carbonyl groups. The —O—C(═O)—O— group can be formed using methods known to those skilled in the art. For example, a compound of Formula (I), wherein R⁶ and R⁷ are both hydroxy groups, can be treated with 1,1′-carbonyldiimidazole (CDI).

In some embodiments, R⁶ and/or R⁷ can be —OC(═O)R¹³ and —OC(═O)R¹⁵, respectively. The —OC(═O)R¹³ and —OC(═O)R¹⁵ groups can be formed at the 2′- and 3′-positions using various methods known to those skilled in the art. As an example, a compound of Formula (I), wherein R⁶ and R⁷ are both hydroxy groups, can be treated with an alkyl anhydride (e.g., acetic anhydride and propionic anhydride) or an alkyl acid chloride (e.g., acetylchloride). If desired, a catalyst can be used to facilitate the reaction. An example of suitable catalyst is 4-dimethylaminopyridine (DMAP). Alternatively, the —OC(═O)R¹³ and —OC(═O)R¹⁵ groups can be formed at the 2′- and 3′-positions by reacting an alkyl acid (e.g. acetic acid and propionic acid) in the presences of a carbodiimide or a coupling reagent. Examples of carbodiimides include, but are not limited to, N,N′-dicyclohexylcarbodiimide (DCC), N,N′-diisopropylcarbodiimide (DIC) and 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide (EDC).

As described herein, B^(1A) can include a carbamate and/or an amide. Those skilled in the art know methods for forming a carbamate and/or an amide on B^(1A). In some embodiments, the carbamate can be formed using 1,1′-carbonyldiimidazole and an alcohol.

B^(1A) can be added to the pentose ring using various methods known to those skilled in the art. In some embodiments, a compound of Formula (B) can be reacted with a nitrogenous base. In some embodiments, R^(3A), R^(3B), R^(4A), R^(5A), R^(6A), R^(7A), R^(8A), R^(9A) and B^(1A) of a compound of Formula (B) can be the same as disclosed herein, with respect to R^(3a), R^(3b), R⁴, R⁵, R⁶, R⁷, R⁸, R⁹ and B¹; and PG¹ can be an appropriate protecting group. In some embodiments, PG¹ can be p-nitrobenzyl group. In some embodiments, any hydroxy groups attached to the pentose ring can be protected with one or more suitable protecting groups. In some embodiments, any hydroxy groups attached to the pentose ring can be protected with benzoyl groups. Examples of nitrogenous bases include an optionally substituted heterocyclic bases described herein, wherein the nitrogen atom (—N) connected to the pentose ring is —NH. If desired, any —NH and/or NH₂ groups present on the nitrogenous base can be protected with one or more suitable protecting groups. Suitable protecting groups are described herein. In some embodiments, the nitrogenous base can be added via a coupling reaction in the presence of a Lewis acid or TMSOTf. Suitable Lewis acids are known to those skilled in the art.

Various methods can be used to make a compound of Formula (I), wherein R¹ is

For example, a thiophosphorochloridate having the general formula of (P(═S)Cl₃) can be transformed into a phosphorus reagent having the general formula, P(═S)LG₃, wherein each LG can be amine-based leaving group. In some embodiments, each LG can be a triazole. The phosphorus reagent having the general formula, P(═S)LG₃, can be reacted with a compound of Formula (I). Using a suitable pyrophosphorylation reagent, the β and γ phosphates can be added. An example of a suitable pyrophosphorylation reagent is tris(tetrabutylammonium) hydrogen pyrophosphate.

During the synthesis of any of the compounds described herein, if desired, any hydroxy groups attached to the pentose ring, and any —NH and/or NH₂ groups present on the B^(1A) can be protected with one or more suitable protecting groups. Suitable protecting groups are described herein. Those skilled in the art will appreciate that groups attached to the pentose ring and any —NH and/or NH₂ groups present on the B^(1A) can be protected with various protecting groups, and any protecting groups present can be exchanged for other protecting groups. The selection and exchange of the protecting groups is within the skill of those of ordinary skill in the art. Any protecting group(s) can also be removed by methods known in the art, for example, with an acid (e.g., a mineral or an organic acid), a base or a fluoride source.

Pharmaceutical Compositions

Some embodiments described herein relates to a pharmaceutical composition, that can include a therapeutically effective amount of one or more compounds described herein (e.g., a compound of Formulae (I) or (Iα)), or a pharmaceutically acceptable salt thereof) and a pharmaceutically acceptable carrier, diluent, excipient or combination thereof. In some embodiments, the pharmaceutical composition can include a single diastereomer of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, (for example, a single diastereomer is present in the pharmaceutical composition at a concentration of greater than 99% compared to the total concentration of the other diastereomers). In other embodiments, the pharmaceutical composition can include a mixture of diastereomers of a compound of Formula (I), or a pharmaceutically acceptable salt thereof. For example, the pharmaceutical composition can include a concentration of one diastereomer of >50%, ≧60%, ≧70%, ≧80%, ≧90%, ≧95%, or ≧98%, as compared to the total concentration of the other diastereomers. In some embodiments, the pharmaceutical composition includes a 1:1 mixture of two diastereomers of a compound of Formula (I), or a pharmaceutically acceptable salt thereof.

The term “pharmaceutical composition” refers to a mixture of one or more compounds disclosed herein with other chemical components, such as diluents or carriers. The pharmaceutical composition facilitates administration of the compound to an organism. Pharmaceutical compositions can also be obtained by reacting compounds with inorganic or organic acids such as hydrochloric acid, hydrobromic acid, sulfuric acid, nitric acid, phosphoric acid, methanesulfonic acid, ethanesulfonic acid, p-toluenesulfonic acid and salicylic acid. Pharmaceutical compositions will generally be tailored to the specific intended route of administration.

The term “physiologically acceptable” defines a carrier, diluent or excipient that does not abrogate the biological activity and properties of the compound.

As used herein, a “carrier” refers to a compound that facilitates the incorporation of a compound into cells or tissues. For example, without limitation, dimethyl sulfoxide (DMSO) is a commonly utilized carrier that facilitates the uptake of many organic compounds into cells or tissues of a subject.

As used herein, a “diluent” refers to an ingredient in a pharmaceutical composition that lacks pharmacological activity but may be pharmaceutically necessary or desirable. For example, a diluent may be used to increase the bulk of a potent drug whose mass is too small for manufacture and/or administration. It may also be a liquid for the dissolution of a drug to be administered by injection, ingestion or inhalation. A common form of diluent in the art is a buffered aqueous solution such as, without limitation, phosphate buffered saline that mimics the composition of human blood.

As used herein, an “excipient” refers to an inert substance that is added to a pharmaceutical composition to provide, without limitation, bulk, consistency, stability, binding ability, lubrication, disintegrating ability etc., to the composition. A “diluent” is a type of excipient.

The pharmaceutical compositions described herein can be administered to a human patient per se, or in pharmaceutical compositions where they are mixed with other active ingredients, as in combination therapy, or carriers, diluents, excipients or combinations thereof. Proper formulation is dependent upon the route of administration chosen. Techniques for formulation and administration of the compounds described herein are known to those skilled in the art.

The pharmaceutical compositions disclosed herein may be manufactured in a manner that is itself known, e.g., by means of conventional mixing, dissolving, granulating, dragee-making, levigating, emulsifying, encapsulating, entrapping or tableting processes. Additionally, the active ingredients are contained in an amount effective to achieve its intended purpose. Many of the compounds used in the pharmaceutical combinations disclosed herein may be provided as salts with pharmaceutically compatible counterions.

Multiple techniques of administering a compound exist in the art including, but not limited to, oral, rectal, topical, aerosol, injection and parenteral delivery, including intramuscular, subcutaneous, intravenous, intramedullary injections, intrathecal, direct intraventricular, intraperitoneal, intranasal and intraocular injections.

One may also administer the compound in a local rather than systemic manner, for example, via injection of the compound directly into the infected area, often in a depot or sustained release formulation. Furthermore, one may administer the compound in a targeted drug delivery system, for example, in a liposome coated with a tissue-specific antibody. The liposomes will be targeted to and taken up selectively by the organ.

The compositions may, if desired, be presented in a pack or dispenser device which may contain one or more unit dosage forms containing the active ingredient. The pack may for example comprise metal or plastic foil, such as a blister pack. The pack or dispenser device may be accompanied by instructions for administration. The pack or dispenser may also be accompanied with a notice associated with the container in form prescribed by a governmental agency regulating the manufacture, use, or sale of pharmaceuticals, which notice is reflective of approval by the agency of the form of the drug for human or veterinary administration. Such notice, for example, may be the labeling approved by the U.S. Food and Drug Administration for prescription drugs, or the approved product insert. Compositions that can include a compound described herein formulated in a compatible pharmaceutical carrier may also be prepared, placed in an appropriate container, and labeled for treatment of an indicated condition.

Methods of Use

One embodiment disclosed herein relates to a method of treating and/or ameliorating a disease or condition that can include administering to a subject a therapeutically effective amount of one or more compounds described herein, such as a compound of Formula (I) (including compounds of Formula (Iα)), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound described herein.

Some embodiments disclosed herein relate to a method of ameliorating or treating a neoplastic disease that can include administering to a subject suffering from a neoplastic disease a therapeutically effective amount of one or more compounds described herein (e.g., a compound of Formulae (I) and/or (Iα), or a pharmaceutically acceptable salt thereof), or a pharmaceutical composition that includes a compound described herein). In an embodiment, the neoplastic disease can be cancer. In some embodiments, the neoplastic disease can be a tumor such as a solid tumor. In an embodiment, the neoplastic disease can be leukemia. Exemplary leukemias include, but are not limited to, acute lymphoblastic leukemia (ALL), acute myeloid leukemia (AML) and juvenile myelomonocytic leukemia (JMML).

Some embodiments disclosed herein relate to a method of inhibiting the growth of a tumor that can include administering to a subject having a tumor a therapeutically effective amount of one or more compounds described herein (for example, a compound of Formulae (I) and/or (Iα)), or a pharmaceutical composition that includes one or more compounds described herein.

Other embodiments disclosed herein relates to a method of ameliorating or treating a viral infection that can include administering to a subject suffering from a viral infection a therapeutically effective amount of one or more compounds described herein (for example, a compound of Formulae (I) and/or (Iα)), or a pharmaceutical composition that includes one or more compounds described herein. In an embodiment, the viral infection can be caused by a virus selected from an adenovirus, an Alphaviridae, an Arbovirus, an Astrovirus, a Bunyaviridae, a Coronaviridae, a Filoviridae, a Flaviviridae, a Hepadnaviridae, a Herpesviridae, an Alphaherpesvirinae, a Betaherpesvirinae, a Gammaherpesvirinae, a Norwalk Virus, an Astroviridae, a Caliciviridae, an Orthomyxoviridae, a Paramyxoviridae, a Paramyxoviruses, a Rubulavirus, a Morbillivirus, a Papovaviridae, a Parvoviridae, a Picornaviridae, an Aphthoviridae, a Cardioviridae, an Enteroviridae, a Coxsackie virus, a Polio Virus, a Rhinoviridae, a Phycodnaviridae, a Poxviridae, a Reoviridae, a Rotavirus, a Retroviridae, an A-Type Retrovirus, an Immunodeficiency Virus, a Leukemia Viruses, an Avian Sarcoma Viruses, a Rhabdoviruses, a Rubiviridae, a Togaviridae an Arenaviridae and/or a Bornaviridae. In some embodiments, the viral infection can be a hepatitis C viral (HCV) infection. In still other embodiments, the viral infection can be HIV.

Some embodiments disclosed herein relate to methods of ameliorating and/or treating a viral infection that can include contacting a cell infected with the virus with an effective amount of one or more compounds described herein, or a pharmaceutically acceptable salt of a compound described herein, or a pharmaceutical composition that includes one or more compounds described herein, or a pharmaceutically acceptable salt thereof. Other embodiments described herein relate to using one or more compounds described herein, or a pharmaceutically acceptable salt of a compound described herein, in the manufacture of a medicament for ameliorating and/or treating a viral infection that can include contacting a cell infected with the virus with an effective amount of said compound(s). Still other embodiments described herein relate to one or more compounds described herein, or a pharmaceutically acceptable salt of a compound described herein, that can be used for ameliorating and/or treating a viral infection by contacting a cell infected with the virus with an effective amount of said compound(s). In some embodiments, the compound can be a compound of Formulae (I) and/or (Iα), or a pharmaceutical acceptable salt thereof. In other embodiments, the compound can be a mono-, di- and/or tri-phosphate of a compound of Formulae (I) and/or (Iα), or a pharmaceutically acceptable salt of the foregoing. In some embodiments, the virus can be a HCV virus.

Some embodiments disclosed herein relate to methods of inhibiting replication of a virus that can include contacting a cell infected with the virus with an effective amount of one or more compounds described herein, or a pharmaceutically acceptable salt of a compound described herein, or a pharmaceutical composition that includes one or more compounds described herein, or a pharmaceutically acceptable salt thereof. Other embodiments described herein relate to using one or more compounds described herein, or a pharmaceutically acceptable salt of a compound described herein, in the manufacture of a medicament for inhibiting replication of a virus that can include contacting a cell infected with the virus with an effective amount of said compound(s). Still other embodiments described herein relate to a compound described herein, or a pharmaceutically acceptable salt of a compound described herein, that can be used for inhibiting replication of a virus by contacting a cell infected with the virus with an effective amount of said compound(s). In some embodiments, the compound can be a compound of Formulae (I) and/or (Iα), or a pharmaceutical acceptable salt thereof. In other embodiments, the compound can be a mono-, di- and/or tri-phosphate of a compound of Formulae (I) and/or (Iα), or a pharmaceutically acceptable salt of the foregoing. In some embodiments, the virus can be a HCV virus.

HCV is an enveloped positive strand RNA virus in the Flaviviridae family. There are various nonstructural proteins of HCV, such as (NS2, NS3, NS4, NS4A, NS4B, NS5A, and NS5B. NS5B is believed to be an RNA-dependent RNA polymerase involved in the replication of HCV RNA.

Some embodiments described herein relate to a method of inhibiting NS5B polymerase activity can include contacting a cell (for example, a cell infected with HCV) with an effective amount of a compound of Formulae (I) and/or (Iα), or a pharmaceutical acceptable salt thereof. Some embodiments described herein relate to a method of inhibiting NS5B polymerase activity can include administering a cell (for example, a cell infected with HCV) with an effective amount of a compound of Formulae (I) and/or (Iα), or a pharmaceutical acceptable salt thereof. In some embodiments, a compound of Formula (I) (including a compound of Formula (Iα)), or a pharmaceutically acceptable salt thereof, can inhibit a RNA dependent RNA polymerase. In some embodiments, a compound of Formula (I) (including a compound of Formula (Iα)), or a pharmaceutically acceptable salt thereof, can inhibit a HCV polymerase (for example, NS5B polymerase).

Some embodiments described herein relate to a method of treating HCV infection in a subject suffering from a HCV infection that can include administering to the subject an effective amount of a compound of Formulae (I) and/or (Iα), or a pharmaceutical acceptable salt thereof, or a pharmaceutical composition that includes an effective amount of a compound of Formulae (I) and/or (Iα), or a pharmaceutical acceptable salt thereof. Some embodiments described herein relate to a method of treating a condition selected from liver fibrosis, liver cirrhosis, and liver cancer in a subject suffering from one or more of the aforementioned liver conditions that can include administering to the subject an effective amount of a compound or a pharmaceutical composition described herein (for example, a compound of Formulae (I) and/or (Iα), or a pharmaceutical acceptable salt thereof). One cause of the liver fibrosis, liver cirrhosis, and/or liver cancer can be a HCV infection. Some embodiments described herein relate to a method of increasing liver function in a subject having a HCV infection that can include administering to the subject an effective amount of a compound or a pharmaceutical composition described herein (for example, a compound of Formulae (I) and/or (Iα), or a pharmaceutical acceptable salt thereof). Also contemplated is a method for reducing or eliminating further virus-caused liver damage in a subject having an HCV infection by administering to the subject an effective amount of a compound or a pharmaceutical composition described herein (for example, a compound of Formulae (I) and/or (Iα), or a pharmaceutical acceptable salt thereof). In one embodiment, this method comprises slowing or halting the progression of liver disease. In another embodiment, the course of the disease is reversed, and stasis or improvement in liver function is contemplated.

There are a variety of genotypes of HCV, and a variety of subtypes within each genotype. For example, at present it is known that there are eleven (numbered 1 through 11) main genotypes of HCV, although others have classified the genotypes as 6 main genotypes. Each of these genotypes is further subdivided into subtypes (1a-1c; 2a-2c; 3a-3b; 4a-4e; 5a; 6a; 7a-7b; 8a-8b; 9a; 10a; and 11a). In some embodiments, an effective amount of a compound of Formulae (I) and/or (Iα), or a pharmaceutical acceptable salt thereof, or a pharmaceutical composition that includes an effective amount of a compound of Formulae (I) and/or (Iα), or a pharmaceutical acceptable salt thereof, can be effective to treat at least one genotype of HCV. In some embodiments, a compound described herein (for example, a compound of Formulae (I) and/or (Iα), or a pharmaceutical acceptable salt thereof) can be effective to treat all 11 genotypes of HCV. In some embodiments, a compound described herein (for example, a compound of Formulae (I) and/or (Iα), or a pharmaceutical acceptable salt thereof) can be effective to treat 3 or more, 5 or more, 7 or more of 9 more genotypes of HCV. In some embodiments, a compound of Formula (I) and/or (Iα), or a pharmaceutical acceptable salt thereof is more effective against a larger number of HCV genotypes than the standard of care. In some embodiments, a compound of Formula (I) and/or (Iα), or a pharmaceutical acceptable salt thereof, is more effective against a particular HCV genotype than the standard of care (such as genotype 1, 2, 3, 4, 5 and/or 6).

Various indicators for determining the effectiveness of a method for treating a HCV infection are known to those skilled in the art. Example of suitable indicators include, but are not limited to, a reduction in viral load, a reduction in viral replication, a reduction in time to seroconversion (virus undetectable in patient serum), an increase in the rate of sustained viral response to therapy, a reduction of morbidity or mortality in clinical outcomes, a reduction in the rate of liver function decrease; stasis in liver function; improvement in liver function; reduction in one or more markers of liver dysfunction, including alanine transaminase, aspartate transaminase, total bilirubin, conjugated bilirubin, gamma glutamyl transpeptidase, and/or other indicator of disease response. Similarly, successful therapy with an effective amount of a compound or a pharmaceutical composition described herein (for example, a compound of Formulae (I) and/or (Iα), or a pharmaceutical acceptable salt thereof) can reduce the incidence of liver cancer in HCV patients.

In some embodiments, an effective amount of a compound of Formulae (I) and/or (Iα), or a pharmaceutically acceptable salt thereof, is an amount that is effective to reduce viral titers to undetectable levels, for example, to about 1000 to about 5000, to about 500 to about 1000, or to about 100 to about 500 genome copies/mL serum. In some embodiments, an effective amount of a compound of Formula (I) and/or (Iα), or a pharmaceutically acceptable salt thereof, is an amount that is effective to reduce viral load compared to the viral load before administration of the compound of Formula (I) and/or (Iα), or a pharmaceutically acceptable salt thereof. For example, wherein the viral load is measured before administration of the compound of Formula (I) and/or (Iα), or a pharmaceutically acceptable salt thereof, and again after completion of the treatment regime with the compound of Formula (I) and/or (Iα), or a pharmaceutically acceptable salt thereof (for example, 1 month after completion). In some embodiments, an effective amount of a compound of Formula (I) and/or (Iα), or a pharmaceutically acceptable salt thereof, can be an amount that is effective to reduce viral load to lower than about 100 genome copies/mL serum. In some embodiments, an effective amount of a compound of Formula (I) and/or (Iα), or a pharmaceutically acceptable salt thereof, is an amount that is effective to achieve a reduction in viral titer in the serum of the subject in the range of about 1.5-log to about a 2.5-log reduction, about a 3-log to about a 4-log reduction, or a greater than about 5-log reduction compared to the viral load before administration of the compound of Formula (I) and/or (Iα), or a pharmaceutically acceptable salt thereof. For example, the viral load can be measured before administration of the compound of Formula (I) and/or (Iα), or a pharmaceutically acceptable salt thereof, and again after completion of the treatment regime with the compound of Formula (I) and/or (Iα), or a pharmaceutically acceptable salt thereof (for example, 1 month after completion).

In some embodiments, a compound of Formula (I) and/or (Iα), or a pharmaceutically acceptable salt thereof, can result in at least a 1, 2, 3, 4, 5, 10, 15, 20, 25, 50, 75, 100-fold or more reduction in the replication of HCV relative to pre-treatment levels in a subject, as determined after completion of the treatment regime (for example 1 month after completion). In some embodiments, a compound of Formula (I) and/or (Iα), or a pharmaceutically acceptable salt thereof, can result in a reduction of the replication of HCV relative to pre-treatment levels in the range of about 2 to about 5 fold, about 10 to about 20 fold, about 15 to about 40 fold, or about 50 to about 100 fold. In some embodiments, a compound of Formula (I) and/or (Iα), or a pharmaceutically acceptable salt thereof, can result in a reduction of HCV replication in the range of 1 to 1.5 log, 1.5 log to 2 log, 2 log to 2.5 log, 2.5 to 3 log, 3 log to 3.5 log or 3.5 to 4 log more reduction of HCV replication compared to the reduction of HCV reduction achieved by pegylated interferon in combination with ribavirin, administered according to the standard of care, or may achieve the same reduction as that standard of care therapy in a shorter period of time, for example, in one month, two months, or three months, as compared to the reduction achieved after six months of standard of care therapy with ribavirin and pegylated interferon.

In some embodiments, an effective amount of a compound of Formula (I) and/or (Iα), or a pharmaceutically acceptable salt thereof, is an amount that is effective to achieve a sustained viral response, for example, non-detectable or substantially non-detectable HCV RNA (e.g., less than about 500, less than about 400, less than about 200, or less than about 100 genome copies per milliliter serum) is found in the subject's serum for a period of at least about one month, at least about two months, at least about three months, at least about four months, at least about five months, or at least about six months following cessation of therapy.

In some embodiments, a therapeutically effective amount of a compound of Formula (I) and/or (Iα), or a pharmaceutically acceptable salt thereof, can reduce a level of a marker of liver fibrosis by at least about 10%, at least about 20%, at least about 25%, at least about 30%, at least about 35%, at least about 40%, at least about 45%, at least about 50%, at least about 55%, at least about 60%, at least about 65%, at least about 70%, at least about 75%, or at least about 80%, or more, compared to the level of the marker in an untreated subject, or to a placebo-treated subject. Methods of measuring serum markers are known to those skilled in the art and include immunological-based methods, e.g., enzyme-linked immunosorbent assays (ELISA), radioimmunoassays, and the like, using antibody specific for a given serum marker. A non-limiting list of examples of a markers includes measuring the levels of serum alanine aminotransferase (ALT), asparatate aminotransferacse (AST), alkaline phosphatase (ALP), gamma-glutamyl transpeptidase (GGT) and total bilirubin (TBIL) using known methods. In general, an ALT level of less than about 45 IU/L (international units/liter), an AST in the range of 10-34 IU/L, ALP in the range of 44-147 IU/L, GGT in the range of 0-51 IU/L, TBIL in the range of 0.3-1.9 mg/dL is considered normal. In some embodiments, an effective amount of a compound of Formula (I) and/or (Iα) is an amount effective to reduce ALT, AST, ALP, GGT and/or TBIL levels to with what is considered a normal level.

Subjects who are clinically diagnosed with HCV infection include “naïve” subjects (e.g., subjects not previously treated for HCV, particularly those who have not previously received IFN-alpha-based and/or ribavirin-based therapy) and individuals who have failed prior treatment for HCV (“treatment failure” subjects). Treatment failure subjects include “non-responders” (i.e., subjects in whom the HCV titer was not significantly or sufficiently reduced by a previous treatment for HCV (≦0.5 log IU/mL), for example, a previous IFN-alpha monotherapy, a previous IFN-alpha and ribavirin combination therapy, or a previous pegylated IFN-alpha and ribavirin combination therapy); and “relapsers” (i.e., subjects who were previously treated for HCV, for example, who received a previous IFN-alpha monotherapy, a previous IFN-alpha and ribavirin combination therapy, or a previous pegylated IFN-alpha and ribavirin combination therapy, whose HCV titer decreased, and subsequently increased).

In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be administered to a treatment failure subject suffering from HCV. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be administered to a non-responder subject suffering from HCV. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be administered to a relapsed subject suffering from HCV.

After a period of time, infectious agents can develop resistance to one or more therapeutic agents. The term “resistance” as used herein refers to a viral strain displaying a delayed, lessened and/or null response to a therapeutic agent(s). For example, after treatment with an antiviral agent, the viral load of a subject infected with a resistant virus may be reduced to a lesser degree compared to the amount in viral load reduction exhibited by a subject infected with a non-resistant strain. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be administered to a subject infected with an HCV strain that is resistant to one or more different anti-HCV agents. In some embodiments, development of resistant HCV strains is delayed when patients are treated with a compound of Formula (I), or a pharmaceutically acceptable salt thereof, compared to the development of HCV strains resistant to other HCV drugs.

In some embodiments, an effective amount of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be administered to a subject for whom other anti-HCV medications are contraindicated. For example, administration of pegylated interferon alpha in combination with ribavirin is contraindicated in subjects with hemoglobinopathies (e.g., thalassemia major, sickle-cell anemia) and other subjects at risk from the hematologic side effects of current therapy. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be provided to a subject that is hypersensitive to interferon or ribavirin.

Some subjects being treated for HCV experience a viral load rebound. The term “viral load rebound” as used herein refers to a sustained ≧0.5 log IU/mL increase of viral load above nadir before the end of treatment, where nadir is a ≧0.5 log IU/mL decrease from baseline. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be administered to a subject experiencing viral load rebound, or can prevent such viral load rebound when used to treat the subject.

The standard of care for treating HCV has been associated with several side effects (adverse events). In some embodiments, a compound of Formula (I) (including a compound of Formula (Iα)), or a pharmaceutically acceptable salt thereof, can decrease the number and/or severity of side effects that can be observed in HCV patients being treated with ribavirin and pegylated interferon according to the standard of care. Examples of side effects include, but are not limited to fever, malaise, tachycardia, chills, headache, arthralgias, myalgias, fatigue, apathy, loss of apetite, nausea, vomiting, cognitive changes, asthenia, drowsiness, lack of initiative, irritability, confusion, depression, severe depression, suicidal ideation, anemia, low white blood cell counts, and thinning of hair. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be provided to a subject that discontinued a HCV therapy because of one or more adverse effects or side effects associated with one or more other HCV agents.

Table 5 provides some embodiments of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, compared to the standard of care. Examples include the following: in some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, results in a percentage of non-responders that is 10% less than the percentage of non-responders receiving the standard of care; in some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, results number of side effects that is in the range of about 10% to about 30% less than compared to the number of side effects experienced by a subject receiving the standard of care; and in some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, results a severity of a side effect (such as one of those described herein) that is 25% less than compared to the severity of the same side effect experienced by a subject receiving the standard of care. Methods of quantifying the severity of a side effect are known to those skilled in the art.

TABLE 5 Percentage Number Severity Percentage Percentage Percentage of viral of of of non- of of load side side responders relapsers resistance rebound effects effects 10% less 10% less 10% less 10% less 10% less 10% less 25% less 25% less 25% less 25% less 25% less 25% less 40% less 40% less 40% less 40% less 40% less 40% less 50% less 50% less 50% less 50% less 50% less 50% less 60% less 60% less 60% less 60% less 60% less 60% less 70% less 70% less 70% less 70% less 70% less 70% less 80% less 80% less 80% less 80% less 80% less 80% less 90% less 90% less 90% less 90% less 90% less 90% less about 10% about 10% about 10% about 10% about 10% about 10% to about to about to about to about to about to about 30% less 30% less 30% less 30% less 30% less 30% less about 20% about 20% about 20% about 20% about 20% about 20% to about to about to about to about to about to about 50% less 50% less 50% less 50% less 50% less 50% less about 30% about 30% about 30% about 30% about 30% about 30% to about to about to about to about to about to about 70% less 70% less 70% less 70% less 70% less 70% less about 20% about 20% about 20% about 20% about 20% about 20% to about to about to about to about to about to about 80% less 80% less 80% less 80% less 80% less 80% less

Yet still other embodiments disclosed herein relates to a method of ameliorating or treating a parasitic disease that can include administering to a subject suffering from a parasitic disease a therapeutically effective amount of one or more compounds described herein (for example, a compound of Formula (I) and/or (Iα)), or a pharmaceutical composition that includes one or more compounds described herein. In an embodiment, the parasite disease can be Chagas' disease.

As used herein, a “subject” refers to an animal that is the object of treatment, observation or experiment. “Animal” includes cold- and warm-blooded vertebrates and invertebrates such as fish, shellfish, reptiles and, in particular, mammals. “Mammal” includes, without limitation, mice, rats, rabbits, guinea pigs, dogs, cats, sheep, goats, cows, horses, primates, such as monkeys, chimpanzees, and apes, and, in particular, humans. In some embodiments, the subject is human.

As used herein, the terms “treating,” “treatment,” “therapeutic,” or “therapy” do not necessarily mean total cure or abolition of the disease or condition. Any alleviation of any undesired signs or symptoms of a disease or condition, to any extent can be considered treatment and/or therapy. Furthermore, treatment may include acts that may worsen the patient's overall feeling of well-being or appearance.

The term “therapeutically effective amount” is used to indicate an amount of an active compound, or pharmaceutical agent, that elicits the biological or medicinal response indicated. For example, a therapeutically effective amount of compound can be the amount needed to prevent, alleviate or ameliorate symptoms of disease or prolong the survival of the subject being treated This response may occur in a tissue, system, animal or human and includes alleviation of the signs or symptoms of the disease being treated. Determination of a therapeutically effective amount is well within the capability of those skilled in the art, in view of the disclosure provided herein. The therapeutically effective amount of the compounds disclosed herein required as a dose will depend on the route of administration, the type of animal, including human, being treated, and the physical characteristics of the specific animal under consideration. The dose can be tailored to achieve a desired effect, but will depend on such factors as weight, diet, concurrent medication and other factors which those skilled in the medical arts will recognize.

As will be readily apparent to one skilled in the art, the useful in vivo dosage to be administered and the particular mode of administration will vary depending upon the age, weight, the severity of the affliction, and mammalian species treated, the particular compounds employed, and the specific use for which these compounds are employed. The determination of effective dosage levels, that is the dosage levels necessary to achieve the desired result, can be accomplished by one skilled in the art using routine methods, for example, human clinical trials and in vitro studies.

The dosage may range broadly, depending upon the desired effects and the therapeutic indication. Alternatively dosages may be based and calculated upon the surface area of the patient, as understood by those of skill in the art. Although the exact dosage will be determined on a drug-by-drug basis, in most cases, some generalizations regarding the dosage can be made. The daily dosage regimen for an adult human patient may be, for example, an oral dose of between 0.01 mg and 3000 mg of each active ingredient, preferably between 1 mg and 700 mg, e.g. 5 to 200 mg. The dosage may be a single one or a series of two or more given in the course of one or more days, as is needed by the subject. In some embodiments, the compounds will be administered for a period of continuous therapy, for example for a week or more, or for months or years. In some embodiments, a compound of Formula (I) (including a compound of Formula (Iα)), or a pharmaceutically acceptable salt thereof, can be administered less frequently compared to the frequency of administration of an agent within the standard of care. In some embodiments, a compound of Formula (I) (including a compound of Formula (Iα)), or a pharmaceutically acceptable salt thereof, can be administered one time per day. For example, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be administered one time per day to a subject suffering from a HCV infection. In some embodiments, the total time of the treatment regime with a compound of Formula (I) (including a compound of Formula (Iα)), or a pharmaceutically acceptable salt thereof, can less compared to the total time of the treatment regime with the standard of care.

In instances where human dosages for compounds have been established for at least some condition, those same dosages may be used, or dosages that are between about 0.1% and 500%, more preferably between about 25% and 250% of the established human dosage. Where no human dosage is established, as will be the case for newly-discovered pharmaceutical compositions, a suitable human dosage can be inferred from ED₅₀ or ID₅₀ values, or other appropriate values derived from in vitro or in vivo studies, as qualified by toxicity studies and efficacy studies in animals.

In cases of administration of a pharmaceutically acceptable salt, dosages may be calculated as the free base. As will be understood by those of skill in the art, in certain situations it may be necessary to administer the compounds disclosed herein in amounts that exceed, or even far exceed, the above-stated, preferred dosage range in order to effectively and aggressively treat particularly aggressive diseases or infections.

Dosage amount and interval may be adjusted individually to provide plasma levels of the active moiety which are sufficient to maintain the modulating effects, or minimal effective concentration (MEC). The MEC will vary for each compound but can be estimated from in vitro data. Dosages necessary to achieve the MEC will depend on individual characteristics and route of administration. However, HPLC assays or bioassays can be used to determine plasma concentrations. Dosage intervals can also be determined using MEC value. Compositions should be administered using a regimen which maintains plasma levels above the MEC for 10-90% of the time, preferably between 30-90% and most preferably between 50-90%. In cases of local administration or selective uptake, the effective local concentration of the drug may not be related to plasma concentration.

It should be noted that the attending physician would know how to and when to terminate, interrupt, or adjust administration due to toxicity or organ dysfunctions. Conversely, the attending physician would also know to adjust treatment to higher levels if the clinical response were not adequate (precluding toxicity). The magnitude of an administrated dose in the management of the disorder of interest will vary with the severity of the condition to be treated and to the route of administration. The severity of the condition may, for example, be evaluated, in part, by standard prognostic evaluation methods. Further, the dose and perhaps dose frequency, will also vary according to the age, body weight, and response of the individual patient. A program comparable to that discussed above may be used in veterinary medicine.

Compounds disclosed herein can be evaluated for efficacy and toxicity using known methods. For example, the toxicology of a particular compound, or of a subset of the compounds, sharing certain chemical moieties, may be established by determining in vitro toxicity towards a cell line, such as a mammalian, and preferably human, cell line. The results of such studies are often predictive of toxicity in animals, such as mammals, or more specifically, humans. Alternatively, the toxicity of particular compounds in an animal model, such as mice, rats, rabbits, or monkeys, may be determined using known methods. The efficacy of a particular compound may be established using several recognized methods, such as in vitro methods, animal models, or human clinical trials. When selecting a model to determine efficacy, the skilled artisan can be guided by the state of the art to choose an appropriate model, dose, route of administration and/or regime.

Combination Therapies

In some embodiments, the compounds disclosed herein, such as a compound of Formula (I) (including compounds of Formula (Iα)), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound described herein, can be used in combination with one or more additional agent(s). Examples of additional agents that can be used in combination with a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, include, but are not limited to, agents currently used in a conventional standard of care for treating HCV, HCV protease inhibitors, HCV polymerase inhibitors, NS5A inhibitors, other antiviral compounds, compounds of Formula (AA) (including mono-, di, and/or tri-phosphates of Formula (AA), pharmaceutically acceptable salts and pharmaceutical compositions that can include a compound of Formula (AA), mono-, di- and/or tri-phosphates thereof, or a pharmaceutically acceptable salt of the foregoing), compounds of Formula (BB) (including pharmaceutically acceptable salts and pharmaceutical compositions that can include a compound of Formula (BB), or a pharmaceutically acceptable salt thereof), compounds of Formula (DD) (including pharmaceutically acceptable salts and pharmaceutical compositions that can include a compound of Formula (DD), or a pharmaceutically acceptable salt thereof), and/or combinations thereof. In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be used with one, two, three or more additional agents described herein. A non-limiting list of examples of combinations of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, is provided in Tables A, B, C and D.

In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be used in combination with an agent(s) currently used in a conventional standard of care therapy. For example, for the treatment of HCV, a compound disclosed herein can be used in combination with Pegylated interferon-alpha-2a (brand name PEGASYS®) and ribavirin, or Pegylated interferon-alpha-2b (brand name PEG-INTRON®) and ribavirin. As another example, a compound disclosed herein can be used in combination with oseltamivir (TAMIFLU®) or zanamivin (RELENZA®) for treating an influenza infection.

In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be substituted for an agent currently used in a conventional standard of care therapy. For example, for the treatment of HCV, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be used in place of ribavirin.

In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be used in combination with an interferon, such as a pegylated interferon. Examples of suitable interferons include, but are not limited to, Pegylated interferon-alpha-2a (brand name PEGASYS®), Pegylated interferon-alpha-2b (brand name PEG-INTRON®), interferon alfacon-1 (brand name INFERGEN®), pegylated interferon lambda and/or a combination thereof.

In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be used in combination with a HCV protease inhibitor. A non-limiting list of example HCV protease inhibitors include the following: VX-950 (TELAPREVIR®), MK-5172, ABT-450, BILN-2061, BI-201335, BMS-650032, SCH 503034 (BOCEPREVIR®), GS-9256, GS-9451, IDX-320, ACH-1625, ACH-2684, TMC-435, ITMN-191 (DANOPREVIR®) and/or a combination thereof. A non-limiting list of example HCV protease inhibitors includes the compounds numbered 1001-1014 in FIG. 2.

In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be used in combination with a HCV polymerase inhibitor. In some embodiments, the HCV polymerase inhibitor can be a nucleoside inhibitor. In other embodiments, the HCV polymerase inhibitor can be a non-nucleoside inhibitor. Examples of suitable nucleoside inhibitors include, but are not limited to, RG7128, PSI-7851, PSI-7977, INX-184, PSI-352938, PSI-661, 4′-azidouridine (including known prodrugs of 4′-azidouridine), GS-6620, IDX-184, and TMC649128 and/or combinations thereof. A non-limiting list of example nucleoside inhibitors includes compounds numbered 2001-2010 in FIG. 3. Examples of suitable non-nucleoside inhibitors include, but are not limited to, ABT-333, ANA-598, VX-222, HCV-796, BI-207127, GS-9190, PF-00868554 (FILIBUVIR®), VX-497 and/or combinations thereof. A non-limiting list of example non-nucleoside inhibitors includes the compounds numbered 3001-3008 in FIG. 4.

In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be used in combination with a NS5A inhibitor. A non-limiting list of example NS5A inhibitors include BMS-790052, PPI-461, ACH-2928, GS-5885, BMS-824393 and/or combinations thereof. A non-limiting list of example NS5A inhibitors includes the compounds numbered 4001-4005 in FIG. 5.

In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be used in combination with other antiviral compounds. Examples of other antiviral compounds include, but are not limited to, Debio-025, MIR-122 and/or combinations thereof. A non-limiting list of example other antiviral compounds includes the compounds numbered 5001-5002 in FIG. 6.

In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be used in combination with a compound of Formula (AA), mono-, di- and/or tri-phosphate thereof, or a pharmaceutically acceptable salt of the foregoing, or a pharmaceutical composition that includes a compound of Formula (AA), mono-, di- and/or tri-phosphate thereof, or a pharmaceutically acceptable salt of the foregoing (see, U.S. Provisional Application Nos. 61/385,425, filed Sep. 22, 2010, and 61/426,467, filed Dec. 22, 2010, the contents of which are incorporated by reference in its entirety):

wherein B^(AA1) can be an optionally substituted heterocyclic base or an optionally substituted heterocyclic base with a protected amino group; R^(AA1) can be an optionally substituted N-linked amino acid or an optionally substituted N-linked amino acid ester derivative; R^(AA2) can be selected from an optionally substituted aryl, an optionally substituted heteroaryl and an optionally substituted heterocyclyl; R^(AA3a) and R^(AA3b) can be independently selected from hydrogen, an optionally substituted C₁₋₆ alkyl, an optionally substituted C₂₋₆ alkenyl, an optionally substituted C₂₋₆ alkynyl, an optionally substituted C₁₋₆ haloalkyl and aryl(C₁₋₆ alkyl), provided that at least one of R^(AA3a) and R^(AA3b) is not hydrogen; or R^(AA3a) and R^(AA3b) can be taken together to form a group selected from an optionally substituted C₃₋₆ cycloalkyl, an optionally substituted C₃₋₆ cycloalkenyl, an optionally substituted C₃₋₆ aryl, and an optionally substituted C₃₋₆ heteroaryl; R^(AA4) can be hydrogen; R^(AA5) be selected from hydrogen, —OR^(AA9) and —OC(═O)R^(AA10); R^(AA6) can be selected from hydrogen, halogen, —OR^(AA11) and —OC(═O)R^(AA12); or R^(AA5) and R^(AA6) can be both oxygen atoms and linked together by a carbonyl group; R^(AA7) can be selected from hydrogen, halogen, an optionally substituted C₁₋₆ alkyl, —OR^(AA13) and —OC(═O)R^(AA14); R^(AA8) can be hydrogen or an optionally substituted C₁₋₆ alkyl; R^(AA9), R^(AA11) and R^(AA13) can be independently selected from hydrogen and an optionally substituted C₁₋₆ alkyl; and R^(AA10), R^(AA12) and R^(AA14) can be independently selected from an optionally substituted C₁₋₆ alkyl and an optionally substituted C₃₋₆ cycloalkyl. A non-limiting list of examples of compounds of Formula (AA), and phosphates thereof, includes the compounds numbered 7000-7077 in FIGS. 8A-8I. In some embodiments, Formula (AA) cannot be compound 7044, 7045, 7046, 7047, 7048, 7049, 7050, 7072, 7073, 7074, 7075, 7076 or 7077.

In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be used in combination with a compound of Formula (BB), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (BB), or a pharmaceutically acceptable salt thereof (see, U.S. Provisional Application No. 61/426,471, filed Dec. 22, 2010, the contents of which are incorporated by reference in its entirety):

wherein B^(BB1) can be an optionally substituted heterocyclic base or an optionally substituted heterocyclic base with a protected amino group; X^(BB) can be O (oxygen) or S (sulfur); R^(BB1) can be selected from —Z^(BB)—R^(BB9), an optionally substituted N-linked amino acid and an optionally substituted N-linked amino acid ester derivative; Z^(BB) can be selected from O (oxygen), S (sulfur) and N(R^(BB10)); R^(BB2) and R^(BB3) can be independently selected from hydrogen, an optionally substituted C₁₋₆ alkyl, an optionally substituted C₂₋₆ alkenyl, an optionally substituted C₂₋₆ alkynyl, an optionally substituted C₁₋₆ haloalkyl and an optionally substituted aryl(C₁₋₆ alkyl); or R^(BB2) and R^(BB3) can be taken together to form a group selected from an optionally substituted C₃₋₆ cycloalkyl, an optionally substituted C₃₋₆ cycloalkenyl, an optionally substituted C₃₋₆ aryl and an optionally substituted C₃₋₆ heteroaryl; R^(BB4) can be selected from hydrogen, halogen, azido, cyano, an optionally substituted C₁₋₆ alkyl, an optionally substituted C₂₋₆ alkenyl, an optionally substituted C₂₋₆ alkynyl and an optionally substituted allenyl; R^(BB5) can be hydrogen or an optionally substituted C₁₋₆ alkyl; R^(BB6) can be selected from hydrogen, halogen, azido, amino, cyano, an optionally substituted C₁₋₆ alkyl, —OR^(BB11) and —OC(═O)R^(BB12); R^(BB7) can be selected from hydrogen, halogen, azido, cyano, an optionally substituted C₁₋₆ alkyl, —OR^(BB13) and —OC(═O)R^(BB14); R^(BB8) can be selected from hydrogen, halogen, azido, cyano, an optionally substituted C₁₋₆ alkyl, —OR^(BB15) and —OC(═O)R^(BB16); R^(BB9) can be selected from an optionally substituted alkyl, an optionally substituted alkenyl, an optionally substituted alkynyl, an optionally substituted cycloalkyl, an optionally substituted cycloalkenyl, an optionally substituted aryl, an optionally substituted heteroaryl, an optionally substituted heterocyclyl, an optionally substituted aryl(C₁₋₆alkyl), an optionally substituted heteroaryl(C₁₋₆alkyl) and an optionally substituted heterocyclyl(C₁₋₆alkyl); R^(BB10) can be selected from hydrogen, an optionally substituted alkyl, an optionally substituted alkenyl, an optionally substituted alkynyl, an optionally substituted cycloalkyl, an optionally substituted cycloalkenyl, an optionally substituted aryl, an optionally substituted heteroaryl, an optionally substituted heterocyclyl, an optionally substituted aryl(C₁₋₆alkyl), an optionally substituted heteroaryl(C₁₋₆alkyl) and an optionally substituted heterocyclyl(C₁₋₆alkyl); R^(BB11), R^(BB13) and R^(BB15) can be independently hydrogen or an optionally substituted C₁₋₆ alkyl; and R^(BB12), R^(BB14) and R^(BB16) can be independently an optionally substituted C₁₋₆ alkyl or an optionally substituted C₃₋₆ cycloalkyl. In some embodiments, at least one of R^(BB2) and R^(BB3) is not hydrogen. A non-limiting list of example compounds of Formula (BB) includes the compound numbered 8000-8012 in FIGS. 9A-9B.

In some embodiments, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be used in combination with a compound of Formula (DD), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (DD), or a pharmaceutically acceptable salt thereof (see, U.S. Publication No. 2010-0249068, filed Mar. 19, 2010, the contents of which are incorporated by reference in its entirety):

wherein each

can be independently a double or single bond; A^(DD1) can be selected from C (carbon), O (oxygen) and S (sulfur); B^(DD1) can be an optionally substituted heterocyclic base or a derivative thereof; D^(DD1) can be selected from C═CH₂, CH₂, O (oxygen), S (sulfur), CHF, and CF₂; R^(DD1) can be hydrogen, an optionally substituted alkyl, an optionally substituted cycloalkyl, an optionally substituted aralkyl, dialkylaminoalkylene, alkyl-C(═O)—, aryl-C(═O)—, alkoxyalkyl-C(═O)—, aryloxyalkyl-C(═O)—, alkylsulfonyl, arylsulfonyl, aralkylsulfonyl,

an —O-linked amino acid, diphosphate, triphosphate or derivatives thereof; R^(DD2) and R^(DD3) can be each independently selected from hydrogen, an optionally substituted C₁₋₆ alkyl, an optionally substituted C₂₋₆ alkenyl, an optionally substituted C₂₋₆ alkynyl and an optionally substituted C₁₋₆ haloalkyl, provided that at least one of R^(DD2) and R^(DD3) cannot be hydrogen; or R^(DD2) and R^(DD3) are taken together to form a group selected from among C₃₋₆ cycloalkyl, C₃₋₆ cycloalkenyl, C₃₋₆ aryl, and a C₃₋₆ heteroaryl; R^(DD4) and R^(DD9) can be independently selected from hydrogen, halogen, —NH₂, —NHR^(DDa1), NR^(DDa1)R^(DDb1), —OR^(DDa1), —SR^(DDa1), —CN, —NC, —N₃, —NO₂, —N(R^(DDc1))—NR^(DDa1)R^(DDb1), —N(R^(DDc1))—OR^(DDa1), —S—SR^(DDa1), —C(—O)R^(DDa1), —C(═O)OR^(DDa1), —C(═O)NR^(DDa1)R^(DDb1), —O—(C═O)R^(DDa1), —O—C(═O)NR^(DDa1), —O—C(═O)NR^(DDa1)R^(DDb1), —N(R^(DDc1))—C(═O)NR^(DDa1)R^(DDb1), —S(═O)R^(DDa1), S(═O)₂R^(DDa1), —O—S(═O)₂NR^(DDa1)R^(DDb1), —N(R^(DDc1))—S(═O)₂NR^(DDa1)R^(DDb1), an optionally substituted C₁₋₆ alkyl, an optionally substituted C₂₋₆ alkenyl, an optionally substituted C₂₋₆ alkynyl, an optionally substituted aralkyl and an —O-linked amino acid; R^(DD5), R^(DD6) and R^(DD7) can be independently absent or selected from hydrogen, halogen, —NH₂, —NHR^(DDa1), NR^(DDa1)R^(DDb1), —OR^(DDa1), —SR^(DDa1), —CN, —NC, —N₃, —NO₂, —N(R^(DDc1))—NR^(DDa1)R^(DDb1), —N(R^(DDc1))—OR^(DDa1), —S—SR^(DDa1), —C(═O)R^(DDa1), —C(═O)OR^(DDa1)—C(═O)NR^(DDa1)R^(DDb1), —O—(C═O)R^(DDa1), —O—C(═O)OR^(DDa1), —O—C(═O)NR^(DDa1)R^(DDb1), N(R^(DDc1))—C(═O)NR^(DDa1)R^(DDb1), —S(═O)R^(DDa1), S(═O)₂R^(DDa1), —O—S(═O)₂NR^(DDa1)R^(DDb1), —N(R^(DDc1))—S(═O)₂NR^(DDa1)R^(DDb1), an optionally substituted C₁₋₆ alkyl, an optionally substituted C₂₋₆ alkenyl, an optionally substituted C₂₋₆ alkynyl, an optionally substituted aralkyl and an —O-linked amino acid; or R^(DD6) and R^(DD7) taken together form —O—C(═O)—O—; R^(DD8) can be absent or selected from the group consisting of hydrogen, halogen, —NH₂, —NHR^(DDa1), NR^(DDa1)R^(DDb1), —OR^(DDa1), —SR^(DDa1), —CN, —NC, —N₃, —NO₂, —N(R^(DDc1))NR^(DDa1)R^(DDb1), N(R^(DDc1))—OR^(DDa1), S—SR^(DDa1), —C(═O)R^(DDa1), —C(═O)OR^(DDa1), —C(═O)NR^(DDa1)R^(DDb1), O—C(═O)OR^(DDa1), —O—C(═O)NR^(DDa1)R^(DDb1), N(R^(DDc1)) C(═O)NR^(DDa1)R^(DDb1), S(═O)R^(DDa1), S(═O)₂R^(DDa1), —O—S(═O)₂NR^(DDa1)R^(DDb1), N(R^(DDc1)) S(═O)₂NR^(DDa1)R^(DDb1), an optionally substituted C₁₋₆ alkyl, an optionally substituted C₂₋₆ alkenyl, an optionally substituted C₂₋₆ alkynyl, an optionally substituted haloalkyl, an optionally substituted hydroxyalkyl and an —O-linked amino acid, or when the bond to R^(DD7) indicated by

is a double bond, then R^(DD7) is a C₂₋₆ alkylidene and R^(DD8) is absent; R^(DDa1), R^(DDb1) and R^(DDc1) can be each independently selected from hydrogen, an optionally substituted alkyl, an optionally substituted alkenyl, an optionally substituted alkynyl, an optionally substituted aryl, an optionally substituted heteroaryl, an optionally substituted aralkyl and an optionally substituted heteroaryl(C₁₋₆ alkyl); R^(DD10) can be selected from O⁻, —OH, an optionally substituted aryloxy or aryl-O—,

alkyl-C(═O)—O—CH₂—O—, alkyl-C(═O)—S—CH₂CH₂—O— and an —N-linked amino acid; R^(DD11) can be selected from O⁻, —OH, an optionally substituted aryloxy or aryl-O—,

alkyl-C(═O)—O—CH₂—O—, alkyl-C(═O)—S—CH₂CH₂—O— and an —N-linked amino acid; each R^(DD12) and each R^(DD13) can be independently —C≡N or an optionally substituted substituent selected from C₁₋₈ organylcarbonyl, C₁₋₈ alkoxycarbonyl and C₁₋₈ organylaminocarbonyl; each R^(DD14) can be hydrogen or an optionally substituted C₁₋₆-alkyl; each m^(DD) can be independently 1 or 2, and if both R^(DD10) and R^(DD11) are

each R^(DD12), each R^(DD13), each R^(DD14) and each m^(DD) can be the same or different. In some embodiments, R^(DD8) can be halogen, —OR^(DDa1), an optionally substituted C₁₋₆ alkyl, an optionally substituted C₂₋₆ alkenyl, an optionally substituted C₂₋₆ alkynyl and an optionally substituted C₁₋₆ haloalkyl.

Some embodiments described herein relate to a method of ameliorating or treating a viral infection that can include contacting a cell infected with the viral infection with a therapeutically effective amount of a compound of Formula (I) (including a compound of Formula (Iα)), or a pharmaceutically acceptable salt thereof, in combination with one or more agents selected from an interferon, ribavirin, a HCV protease inhibitor, a HCV polymerase inhibitor, a NS5A inhibitor, an antiviral compound, a compound of Formula (AA), a mono-, di, and/or tri-phosphate thereof, a compound of Formula (BB), and a compound of Formula (DD), or a pharmaceutically acceptable salt of any of the aforementioned compounds.

Some embodiments described herein relate to a method of ameliorating or treating a viral infection that can include administering to a subject suffering from the viral infection a therapeutically effective amount of a compound of Formula (I) (including a compound of Formula (Iα)), or a pharmaceutically acceptable salt thereof, in combination with one or more agents selected from an interferon, ribavirin, a HCV protease inhibitor, a HCV polymerase inhibitor, a NS5A inhibitor, an antiviral compound, a compound of Formula (AA), a mono-, di, and/or tri-phosphate thereof, a compound of Formula (BB), and a compound of Formula (DD), or a pharmaceutically acceptable salt of any of the aforementioned compounds.

Some embodiments described herein relate to a method of inhibiting viral replication of a virus that can include contacting a cell infected with the virus with an effective amount of a compound of Formula (I) (including a compound of Formula (Iα)), or a pharmaceutically acceptable salt thereof, in combination with one or more agents selected from an interferon, ribavirin, a HCV protease inhibitor, a HCV polymerase inhibitor, a NS5A inhibitor, an antiviral compound, a compound of Formula (AA), a mono-, di, and/or tri-phosphate thereof, a compound of Formula (BB), and a compound of Formula (DD), or a pharmaceutically acceptable salt of any of the aforementioned compounds.

Some embodiments described herein relate to a method of ameliorating or treating a viral infection that can include contacting a cell infected with the viral infection with a therapeutically effective amount of a compound of Formula (I) (including a compound of Formula (Iα)), or a pharmaceutically acceptable salt thereof, in combination with one or more agents selected from an interferon, ribavirin, a HCV protease inhibitor, a HCV polymerase inhibitor, a NS5A inhibitor, an antiviral compound, a compound of Formula (AA), a compound of Formula (BB), and a compound of Formula (DD), or a pharmaceutically acceptable salt of any of the aforementioned compounds.

Some embodiments described herein relate to a method of ameliorating or treating a viral infection that can include administering to a subject suffering from the viral infection a therapeutically effective amount of a compound of Formula (I) (including a compound of Formula (Iα)), or a pharmaceutically acceptable salt thereof, in combination with one or more agents selected from an interferon, ribavirin, a HCV protease inhibitor, a HCV polymerase inhibitor, a NS5A inhibitor, an antiviral compound, a compound of Formula (AA), a compound of Formula (BB), and a compound of Formula (DD), or a pharmaceutically acceptable salt of any of the aforementioned compounds.

Some embodiments described herein relate to a method of inhibiting viral replication of a virus that can include contacting a cell infected with the virus with an effective amount of a compound of Formula (I) (including a compound of Formula (Iα)), or a pharmaceutically acceptable salt thereof, in combination with one or more agents selected from an interferon, ribavirin, a HCV protease inhibitor, a HCV polymerase inhibitor, a NS5A inhibitor, an antiviral compound, a compound of Formula (AA), a compound of Formula (BB), and a compound of Formula (DD), or a pharmaceutically acceptable salt of any of the aforementioned compounds.

In some embodiments, a compound of Formula (I) (including a compound of Formula (Iα)), or a pharmaceutically acceptable salt thereof, can be administered with one or more additional agent(s) together in a single pharmaceutical composition. In some embodiments, a compound of Formula (I) (including a compound of Formula (Iα)), or a pharmaceutically acceptable salt the thereof, can be administered with one or more additional agent(s) as two or more separate pharmaceutical compositions. For example, a compound of Formula (I) (including a compound of Formula (Iα)), or a pharmaceutically acceptable salt thereof, can be administered in one pharmaceutical composition, and at least one of the additional agents can be administered in a second pharmaceutical composition. If there are at least two additional agents, one or more of the additional agents can be in a first pharmaceutical composition that includes a compound of Formula (I) (including a compound of Formula (Iα)), or a pharmaceutically acceptable salt thereof, and at least one of the other additional agent(s) can be in a second pharmaceutical composition.

The dosing amount(s) and dosing schedule(s) when using a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, and one or more additional agents are within the knowledge of those skilled in the art. For example, when performing a conventional standard of care therapy using art-recognized dosing amounts and dosing schedules, a compound of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound of Formula (I), or a pharmaceutically acceptable salt thereof, can be administered in addition to that therapy, or in place of one of the agents of a combination therapy, using effective amounts and dosing protocols as described herein.

The order of administration of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, with one or more additional agent(s) can vary. In some embodiments, a compound of Formula (I) (including a compound of Formula (Iα)), or a pharmaceutically acceptable salt thereof, can be administered prior to all additional agents. In other embodiments, a compound of Formula (I) (including a compound of Formula (Iα)), or a pharmaceutically acceptable salt thereof, can be administered prior to at least one additional agent. In still other embodiments, a compound of Formula (I) (including a compound of Formula (Iα)), or a pharmaceutically acceptable salt thereof, can be administered concomitantly with one or more additional agent(s). In yet still other embodiments, a compound of Formula (I) (including a compound of Formula (Iα)), or a pharmaceutically acceptable salt thereof, can be administered subsequent to the administration of at least one additional agent. In some embodiments, a compound of Formula (I) (including a compound of Formula (Iα)), or a pharmaceutically acceptable salt thereof, can be administered subsequent to the administration of all additional agents.

In some embodiments, the combination of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, in combination with one or more additional agent(s) in FIGS. 2-6 and 8-10 (including pharmaceutically acceptable salts and prodrugs thereof) can result in an additive effect. In some embodiments, the combination of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, in combination with one or more additional agent(s) in FIGS. 2-6 and 8-10 (including pharmaceutically acceptable salts and prodrugs thereof) can result in a synergistic effect. In some embodiments, the combination of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, in combination with one or more additional agent(s) in FIGS. 2-6 and 8-10 (including pharmaceutically acceptable salts and prodrugs thereof) can result in a strongly synergistic effect. In some embodiments, the combination of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, in combination with one or more additional agent(s) in FIGS. 2-6 and 8-10 (including pharmaceutically acceptable salts and prodrugs thereof) is not antagonistic.

As used herein, the term “antagonistic” means that the activity of the combination of compounds is less compared to the sum of the activities of the compounds in combination when the activity of each compound is determined individually (i.e. as a single compound). As used herein, the term “synergistic effect” means that the activity of the combination of compounds is greater than the sum of the individual activities of the compounds in the combination when the activity of each compound is determined individually. As used herein, the term “additive effect” means that the activity of the combination of compounds is about equal to the sum of the individual activities of the compound in the combination when the activity of each compound is determined individually.

A potential advantage of utilizing a compound of Formula (I), or a pharmaceutically acceptable salt thereof, in combination with one or more additional agent(s) in FIGS. 2-6 and 8-10 (including pharmaceutically acceptable salts and prodrugs thereof) may be a reduction in the required amount(s) of one or more compounds of FIGS. 2-6 and 8-10 (including pharmaceutically acceptable salts and prodrugs thereof) that is effective in treating a disease condition disclosed herein (for example, HCV), as compared to the amount required to achieve same therapeutic result when one or more compounds of FIGS. 2-6 and 8-10 (including pharmaceutically acceptable salts and prodrugs thereof) are administered without a compound of Formula (I), or a pharmaceutically acceptable salt thereof. For example, the amount of a compound in FIGS. 2-6 and 8-10 (including a pharmaceutically acceptable salt and prodrug thereof), can be less compared to the amount of the compound in FIGS. 2-6 and 8-10 (including a pharmaceutically acceptable salt and prodrug thereof), needed to achieve the same viral load reduction when administered as a monotherapy. Another potential advantage of utilizing a compound of Formula (I), or a pharmaceutically acceptable salt thereof, in combination with one or more additional agent(s) in FIGS. 2-6 and 8-10 (including pharmaceutically acceptable salts and prodrugs thereof) is that the use of two or more compounds having different mechanism of actions can create a higher barrier to the development of resistant viral strains compared to the barrier when a compound is administered as monotherapy.

Additional advantages of utilizing a compound of Formula (I), or a pharmaceutically acceptable salt thereof, in combination with one or more additional agent(s) in FIGS. 2-6 and 8-10 (including pharmaceutically acceptable salts and prodrugs thereof) may include little to no cross resistance between a compound of Formula (I), or a pharmaceutically acceptable salt thereof, and one or more additional agent(s) in FIGS. 2-6 and 8-10 (including pharmaceutically acceptable salts and prodrugs thereof) thereof; different routes for elimination of a compound of Formula (I), or a pharmaceutically acceptable salt thereof, and one or more additional agent(s) in FIGS. 2-6 and 8-10 (including pharmaceutically acceptable salts and prodrugs thereof); little to no overlapping toxicities between a compound of Formula (I), or a pharmaceutically acceptable salt thereof, and one or more additional agent(s) in FIGS. 2-6 and 8-10 (including pharmaceutically acceptable salts and prodrugs thereof); little to no significant effects on cytochrome P450; and/or little to no pharmacokinetic interactions between a compound of Formula (I), or a pharmaceutically acceptable salt thereof, and one or more additional agent(s) in FIGS. 2-6 and 8-10 (including pharmaceutically acceptable salts and prodrugs thereof).

A non-limiting list of example combination of compounds of Formula (I), or a pharmaceutically acceptable salt thereof, or a pharmaceutical composition that includes a compound described herein, with one or more additional agent(s) are provided in Tables A, B, C and D. Each numbered X and Y compound in Tables A, B, C and D has a corresponding name and/or structure provided in FIGS. 2 to 10. The numbered compounds in Tables A, B, C and D includes pharmaceutically acceptable salts of the compounds and pharmaceutical compositions containing the compounds or a pharmaceutically acceptable salt thereof. For example, 1001 includes the compound corresponding to 1001, pharmaceutically acceptable salts thereof, and pharmaceutical compositions that include compound 1001 and/or a pharmaceutically acceptable salt thereof. The combinations exemplified in Tables A, B, C and D are designated by the formula X:Y, which represents a combination of a compound X with a compound Y. For example, the combination designated as 1001:6001 in Table A represents a combination of compound 1001 with compound 6001, including pharmaceutically acceptable salts of compound 1001 and/or 6001, and pharmaceutical compositions including compound 1001 and 6001 (including pharmaceutical compositions that include pharmaceutically acceptable salts of compound 1001 and/or compound 6001). Thus, the combination designated as 1001:6001 in Table A represents the combination of Telaprevir (compound 1001, as shown in FIG. 2) and

(compound 6001, as shown in FIG. 7A), including pharmaceutically acceptable salts of compound 1001 and/or 6001, and pharmaceutical compositions including compound 1001 and 6001 (including pharmaceutical compositions that include pharmaceutically acceptable salts of compound 1001 and/or compound 6001). Each of the combinations provided in Tables A, B, C and D can be used with one, two, three or more additional agents described herein. In some embodiments, embodiments described herein, the combination of agents can be used to treat, amerliorate and/or inhibit a virus and/or a viral infection, wherein the virus can be HCV and the viral infection can be an HCV viral infection.

TABLE A Example combinations of a compound X with a compound Y. 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1009:6045 1009:6046 1009:6047 1009:6048 1010:6042 1010:6043 1010:6044 1010:6045 1010:6046 1010:6047 1010:6048 1011:6042 1011:6043 1011:6044 1011:6045 1011:6046 1011:6047 1011:6048 1012:6042 1012:6043 1012:6044 1012:6045 1012:6046 1012:6047 1012:6048 1013:6042 1013:6043 1013:6044 1013:6045 1013:6046 1013:6047 1013:6048 1014:6042 1014:6043 1014:6044 1014:6045 1014:6046 1014:6047 1014:6048 2001:6042 2001:6043 2001:6044 2001:6045 2001:6046 2001:6047 2001:6048 2002:6042 2002:6043 2002:6044 2002:6045 2002:6046 2002:6047 2002:6048 2003:6042 2003:6043 2003:6044 2003:6045 2003:6046 2003:6047 2003:6048 2004:6042 2004:6043 2004:6044 2004:6045 2004:6046 2004:6047 2004:6048 2005:6042 2005:6043 2005:6044 2005:6045 2005:6046 2005:6047 2005:6048 2006:6042 2006:6043 2006:6044 2006:6045 2006:6046 2006:6047 2006:6048 2007:6042 2007:6043 2007:6044 2007:6045 2007:6046 2007:6047 2007:6048 2008:6042 2008:6043 2008:6044 2008:6045 2008:6046 2008:6047 2008:6048 2009:6042 2009:6043 2009:6044 2009:6045 2009:6046 2009:6047 2009:6048 2010:6042 2010:6043 2010:6044 2010:6045 2010:6046 2010:6047 2010:6048 3001:6042 3001:6043 3001:6044 3001:6045 3001:6046 3001:6047 3001:6048 3002:6042 3002:6043 3002:6044 3002:6045 3002:6046 3002:6047 3002:6048 3003:6042 3003:6043 3003:6044 3003:6045 3003:6046 3003:6047 3003:6048 3004:6042 3004:6043 3004:6044 3004:6045 3004:6046 3004:6047 3004:6048 3005:6042 3005:6043 3005:6044 3005:6045 3005:6046 3005:6047 3005:6048 3006:6042 3006:6043 3006:6044 3006:6045 3006:6046 3006:6047 3006:6048 3007:6042 3007:6043 3007:6044 3007:6045 3007:6046 3007:6047 3007:6048 3008:6042 3008:6043 3008:6044 3008:6045 3008:6046 3008:6047 3008:6048 4001:6042 4001:6043 4001:6044 4001:6045 4001:6046 4001:6047 4001:6048 4002:6042 4002:6043 4002:6044 4002:6045 4002:6046 4002:6047 4002:6048 4003:6042 4003:6043 4003:6044 4003:6045 4003:6046 4003:6047 4003:6048 4004:6042 4004:6043 4004:6044 4004:6045 4004:6046 4004:6047 4004:6048 4005:6042 4005:6043 4005:6044 4005:6045 4005:6046 4005:6047 4005:6048 5001:6042 5001:6043 5001:6044 5001:6045 5001:6046 5001:6047 5001:6048 5002:6042 5002:6043 5002:6044 5002:6045 5002:6046 5002:6047 5002:6048 1001:6049 1001:6050 1001:6051 1001:6052 1001:6053 1001:6054 1001:6055 1002:6049 1002:6050 1002:6051 1002:6052 1002:6053 1002:6054 1002:6055 1003:6049 1003:6050 1003:6051 1003:6052 1003:6053 1003:6054 1003:6055 1004:6049 1004:6050 1004:6051 1004:6052 1004:6053 1004:6054 1004:6055 1005:6049 1005:6050 1005:6051 1005:6052 1005:6053 1005:6054 1005:6055 1006:6049 1006:6050 1006:6051 1006:6052 1006:6053 1006:6054 1006:6055 1007:6049 1007:6050 1007:6051 1007:6052 1007:6053 1007:6054 1007:6055 1008:6049 1008:6050 1008:6051 1008:6052 1008:6053 1008:6054 1008:6055 1009:6049 1009:6050 1009:6051 1009:6052 1009:6053 1009:6054 1009:6055 1010:6049 1010:6050 1010:6051 1010:6052 1010:6053 1010:6054 1010:6055 1011:6049 1011:6050 1011:6051 1011:6052 1011:6053 1011:6054 1011:6055 1012:6049 1012:6050 1012:6051 1012:6052 1012:6053 1012:6054 1012:6055 1013:6049 1013:6050 1013:6051 1013:6052 1013:6053 1013:6054 1013:6055 1014:6049 1014:6050 1014:6051 1014:6052 1014:6053 1014:6054 1014:6055 2001:6049 2001:6050 2001:6051 2001:6052 2001:6053 2001:6054 2001:6055 2002:6049 2002:6050 2002:6051 2002:6052 2002:6053 2002:6054 2002:6055 2003:6049 2003:6050 2003:6051 2003:6052 2003:6053 2003:6054 2003:6055 2004:6049 2004:6050 2004:6051 2004:6052 2004:6053 2004:6054 2004:6055 2005:6049 2005:6050 2005:6051 2005:6052 2005:6053 2005:6054 2005:6055 2006:6049 2006:6050 2006:6051 2006:6052 2006:6053 2006:6054 2006:6055 2007:6049 2007:6050 2007:6051 2007:6052 2007:6053 2007:6054 2007:6055 2008:6049 2008:6050 2008:6051 2008:6052 2008:6053 2008:6054 2008:6055 2009:6049 2009:6050 2009:6051 2009:6052 2009:6053 2009:6054 2009:6055 2010:6049 2010:6050 2010:6051 2010:6052 2010:6053 2010:6054 2010:6055 3001:6049 3001:6050 3001:6051 3001:6052 3001:6053 3001:6054 3001:6055 3002:6049 3002:6050 3002:6051 3002:6052 3002:6053 3002:6054 3002:6055 3003:6049 3003:6050 3003:6051 3003:6052 3003:6053 3003:6054 3003:6055 3004:6049 3004:6050 3004:6051 3004:6052 3004:6053 3004:6054 3004:6055 3005:6049 3005:6050 3005:6051 3005:6052 3005:6053 3005:6054 3005:6055 3006:6049 3006:6050 3006:6051 3006:6052 3006:6053 3006:6054 3006:6055 3007:6049 3007:6050 3007:6051 3007:6052 3007:6053 3007:6054 3007:6055 3008:6049 3008:6050 3008:6051 3008:6052 3008:6053 3008:6054 3008:6055 4001:6049 4001:6050 4001:6051 4001:6052 4001:6053 4001:6054 4001:6055 4002:6049 4002:6050 4002:6051 4002:6052 4002:6053 4002:6054 4002:6055 4003:6049 4003:6050 4003:6051 4003:6052 4003:6053 4003:6054 4003:6055 4004:6049 4004:6050 4004:6051 4004:6052 4004:6053 4004:6054 4004:6055 4005:6049 4005:6050 4005:6051 4005:6052 4005:6053 4005:6054 4005:6055 5001:6049 5001:6050 5001:6051 5001:6052 5001:6053 5001:6054 5001:6055 5002:6049 5002:6050 5002:6051 5002:6052 5002:6053 5002:6054 5002:6055 1001:6056 1001:6057 1001:6058 1001:6059 1001:6060 1001:6061 1001:6062 1002:6056 1002:6057 1002:6058 1002:6059 1002:6060 1002:6061 1002:6062 1003:6056 1003:6057 1003:6058 1003:6059 1003:6060 1003:6061 1003:6062 1004:6056 1004:6057 1004:6058 1004:6059 1004:6060 1004:6061 1004:6062 1005:6056 1005:6057 1005:6058 1005:6059 1005:6060 1005:6061 1005:6062 1006:6056 1006:6057 1006:6058 1006:6059 1006:6060 1006:6061 1006:6062 1007:6056 1007:6057 1007:6058 1007:6059 1007:6060 1007:6061 1007:6062 1008:6056 1008:6057 1008:6058 1008:6059 1008:6060 1008:6061 1008:6062 1009:6056 1009:6057 1009:6058 1009:6059 1009:6060 1009:6061 1009:6062 1010:6056 1010:6057 1010:6058 1010:6059 1010:6060 1010:6061 1010:6062 1011:6056 1011:6057 1011:6058 1011:6059 1011:6060 1011:6061 1011:6062 1012:6056 1012:6057 1012:6058 1012:6059 1012:6060 1012:6061 1012:6062 1013:6056 1013:6057 1013:6058 1013:6059 1013:6060 1013:6061 1013:6062 1014:6056 1014:6057 1014:6058 1014:6059 1014:6060 1014:6061 1014:6062 2001:6056 2001:6057 2001:6058 2001:6059 2001:6060 2001:6061 2001:6062 2002:6056 2002:6057 2002:6058 2002:6059 2002:6060 2002:6061 2002:6062 2003:6056 2003:6057 2003:6058 2003:6059 2003:6060 2003:6061 2003:6062 2004:6056 2004:6057 2004:6058 2004:6059 2004:6060 2004:6061 2004:6062 2005:6056 2005:6057 2005:6058 2005:6059 2005:6060 2005:6061 2005:6062 2006:6056 2006:6057 2006:6058 2006:6059 2006:6060 2006:6061 2006:6062 2007:6056 2007:6057 2007:6058 2007:6059 2007:6060 2007:6061 2007:6062 2008:6056 2008:6057 2008:6058 2008:6059 2008:6060 2008:6061 2008:6062 2009:6056 2009:6057 2009:6058 2009:6059 2009:6060 2009:6061 2009:6062 2010:6056 2010:6057 2010:6058 2010:6059 2010:6060 2010:6061 2010:6062 3001:6056 3001:6057 3001:6058 3001:6059 3001:6060 3001:6061 3001:6062 3002:6056 3002:6057 3002:6058 3002:6059 3002:6060 3002:6061 3002:6062 3003:6056 3003:6057 3003:6058 3003:6059 3003:6060 3003:6061 3003:6062 3004:6056 3004:6057 3004:6058 3004:6059 3004:6060 3004:6061 3004:6062 3005:6056 3005:6057 3005:6058 3005:6059 3005:6060 3005:6061 3005:6062 3006:6056 3006:6057 3006:6058 3006:6059 3006:6060 3006:6061 3006:6062 3007:6056 3007:6057 3007:6058 3007:6059 3007:6060 3007:6061 3007:6062 3008:6056 3008:6057 3008:6058 3008:6059 3008:6060 3008:6061 3008:6062 4001:6056 4001:6057 4001:6058 4001:6059 4001:6060 4001:6061 4001:6062 4002:6056 4002:6057 4002:6058 4002:6059 4002:6060 4002:6061 4002:6062 4003:6056 4003:6057 4003:6058 4003:6059 4003:6060 4003:6061 4003:6062 4004:6056 4004:6057 4004:6058 4004:6059 4004:6060 4004:6061 4004:6062 4005:6056 4005:6057 4005:6058 4005:6059 4005:6060 4005:6061 4005:6062 5001:6056 5001:6057 5001:6058 5001:6059 5001:6060 5001:6061 5001:6062 5002:6056 5002:6057 5002:6058 5002:6059 5002:6060 5002:6061 5002:6062 1001:6063 1001:6064 1001:6065 1001:6066 1001:6067 1001:6068 1001:6069 1002:6063 1002:6064 1002:6065 1002:6066 1002:6067 1002:6068 1002:6069 1003:6063 1003:6064 1003:6065 1003:6066 1003:6067 1003:6068 1003:6069 1004:6063 1004:6064 1004:6065 1004:6066 1004:6067 1004:6068 1004:6069 1005:6063 1005:6064 1005:6065 1005:6066 1005:6067 1005:6068 1005:6069 1006:6063 1006:6064 1006:6065 1006:6066 1006:6067 1006:6068 1006:6069 1007:6063 1007:6064 1007:6065 1007:6066 1007:6067 1007:6068 1007:6069 1008:6063 1008:6064 1008:6065 1008:6066 1008:6067 1008:6068 1008:6069 1009:6063 1009:6064 1009:6065 1009:6066 1009:6067 1009:6068 1009:6069 1010:6063 1010:6064 1010:6065 1010:6066 1010:6067 1010:6068 1010:6069 1011:6063 1011:6064 1011:6065 1011:6066 1011:6067 1011:6068 1011:6069 1012:6063 1012:6064 1012:6065 1012:6066 1012:6067 1012:6068 1012:6069 1013:6063 1013:6064 1013:6065 1013:6066 1013:6067 1013:6068 1013:6069 1014:6063 1014:6064 1014:6065 1014:6066 1014:6067 1014:6068 1014:6069 2001:6063 2001:6064 2001:6065 2001:6066 2001:6067 2001:6068 2001:6069 2002:6063 2002:6064 2002:6065 2002:6066 2002:6067 2002:6068 2002:6069 2003:6063 2003:6064 2003:6065 2003:6066 2003:6067 2003:6068 2003:6069 2004:6063 2004:6064 2004:6065 2004:6066 2004:6067 2004:6068 2004:6069 2005:6063 2005:6064 2005:6065 2005:6066 2005:6067 2005:6068 2005:6069 2006:6063 2006:6064 2006:6065 2006:6066 2006:6067 2006:6068 2006:6069 2007:6063 2007:6064 2007:6065 2007:6066 2007:6067 2007:6068 2007:6069 2008:6063 2008:6064 2008:6065 2008:6066 2008:6067 2008:6068 2008:6069 2009:6063 2009:6064 2009:6065 2009:6066 2009:6067 2009:6068 2009:6069 2010:6063 2010:6064 2010:6065 2010:6066 2010:6067 2010:6068 2010:6069 3001:6063 3001:6064 3001:6065 3001:6066 3001:6067 3001:6068 3001:6069 3002:6063 3002:6064 3002:6065 3002:6066 3002:6067 3002:6068 3002:6069 3003:6063 3003:6064 3003:6065 3003:6066 3003:6067 3003:6068 3003:6069 3004:6063 3004:6064 3004:6065 3004:6066 3004:6067 3004:6068 3004:6069 3005:6063 3005:6064 3005:6065 3005:6066 3005:6067 3005:6068 3005:6069 3006:6063 3006:6064 3006:6065 3006:6066 3006:6067 3006:6068 3006:6069 3007:6063 3007:6064 3007:6065 3007:6066 3007:6067 3007:6068 3007:6069 3008:6063 3008:6064 3008:6065 3008:6066 3008:6067 3008:6068 3008:6069 4001:6063 4001:6064 4001:6065 4001:6066 4001:6067 4001:6068 4001:6069 4002:6063 4002:6064 4002:6065 4002:6066 4002:6067 4002:6068 4002:6069 4003:6063 4003:6064 4003:6065 4003:6066 4003:6067 4003:6068 4003:6069 4004:6063 4004:6064 4004:6065 4004:6066 4004:6067 4004:6068 4004:6069 4005:6063 4005:6064 4005:6065 4005:6066 4005:6067 4005:6068 4005:6069 5001:6063 5001:6064 5001:6065 5001:6066 5001:6067 5001:6068 5001:6069 5002:6063 5002:6064 5002:6065 5002:6066 5002:6067 5002:6068 5002:6069 1001:6070 1001:6071 1001:6072 1001:6073 1001:6074 1001:6075 1001:6076 1002:6070 1002:6071 1002:6072 1002:6073 1002:6074 1002:6075 1002:6076 1003:6070 1003:6071 1003:6072 1003:6073 1003:6074 1003:6075 1003:6076 1004:6070 1004:6071 1004:6072 1004:6073 1004:6074 1004:6075 1004:6076 1005:6070 1005:6071 1005:6072 1005:6073 1005:6074 1005:6075 1005:6076 1006:6070 1006:6071 1006:6072 1006:6073 1006:6074 1006:6075 1006:6076 1007:6070 1007:6071 1007:6072 1007:6073 1007:6074 1007:6075 1007:6076 1008:6070 1008:6071 1008:6072 1008:6073 1008:6074 1008:6075 1008:6076 1009:6070 1009:6071 1009:6072 1009:6073 1009:6074 1009:6075 1009:6076 1010:6070 1010:6071 1010:6072 1010:6073 1010:6074 1010:6075 1010:6076 1011:6070 1011:6071 1011:6072 1011:6073 1011:6074 1011:6075 1011:6076 1012:6070 1012:6071 1012:6072 1012:6073 1012:6074 1012:6075 1012:6076 1013:6070 1013:6071 1013:6072 1013:6073 1013:6074 1013:6075 1013:6076 1014:6070 1014:6071 1014:6072 1014:6073 1014:6074 1014:6075 1014:6076 2001:6070 2001:6071 2001:6072 2001:6073 2001:6074 2001:6075 2001:6076 2002:6070 2002:6071 2002:6072 2002:6073 2002:6074 2002:6075 2002:6076 2003:6070 2003:6071 2003:6072 2003:6073 2003:6074 2003:6075 2003:6076 2004:6070 2004:6071 2004:6072 2004:6073 2004:6074 2004:6075 2004:6076 2005:6070 2005:6071 2005:6072 2005:6073 2005:6074 2005:6075 2005:6076 2006:6070 2006:6071 2006:6072 2006:6073 2006:6074 2006:6075 2006:6076 2007:6070 2007:6071 2007:6072 2007:6073 2007:6074 2007:6075 2007:6076 2008:6070 2008:6071 2008:6072 2008:6073 2008:6074 2008:6075 2008:6076 2009:6070 2009:6071 2009:6072 2009:6073 2009:6074 2009:6075 2009:6076 2010:6070 2010:6071 2010:6072 2010:6073 2010:6074 2010:6075 2010:6076 3001:6070 3001:6071 3001:6072 3001:6073 3001:6074 3001:6075 3001:6076 3002:6070 3002:6071 3002:6072 3002:6073 3002:6074 3002:6075 3002:6076 3003:6070 3003:6071 3003:6072 3003:6073 3003:6074 3003:6075 3003:6076 3004:6070 3004:6071 3004:6072 3004:6073 3004:6074 3004:6075 3004:6076 3005:6070 3005:6071 3005:6072 3005:6073 3005:6074 3005:6075 3005:6076 3006:6070 3006:6071 3006:6072 3006:6073 3006:6074 3006:6075 3006:6076 3007:6070 3007:6071 3007:6072 3007:6073 3007:6074 3007:6075 3007:6076 3008:6070 3008:6071 3008:6072 3008:6073 3008:6074 3008:6075 3008:6076 4001:6070 4001:6071 4001:6072 4001:6073 4001:6074 4001:6075 4001:6076 4002:6070 4002:6071 4002:6072 4002:6073 4002:6074 4002:6075 4002:6076 4003:6070 4003:6071 4003:6072 4003:6073 4003:6074 4003:6075 4003:6076 4004:6070 4004:6071 4004:6072 4004:6073 4004:6074 4004:6075 4004:6076 4005:6070 4005:6071 4005:6072 4005:6073 4005:6074 4005:6075 4005:6076 5001:6070 5001:6071 5001:6072 5001:6073 5001:6074 5001:6075 5001:6076 5002:6070 5002:6071 5002:6072 5002:6073 5002:6074 5002:6075 5002:6076 1001:6077 1014:6077 3003:6077 1001:6078 1014:6078 3003:6078 — 1002:6077 2001:6077 3004:6077 1002:6078 2001:6078 3004:6078 1003:6077 2002:6077 3005:6077 1003:6078 2002:6078 3005:6078 1004:6077 2003:6077 3006:6077 1004:6078 2003:6078 3006:6078 1005:6077 2004:6077 3007:6077 1005:6078 2004:6078 3007:6078 1006:6077 2005:6077 3008:6077 1006:6078 2005:6078 3008:6078 1007:6077 2006:6077 4001:6077 1007:6078 2006:6078 4001:6078 1008:6077 2007:6077 4002:6077 1008:6078 2007:6078 4002:6078 1009:6077 2008:6077 4003:6077 1009:6078 2008:6078 4003:6078 1010:6077 2009:6077 4004:6077 1010:6078 2009:6078 4004:6078 1011:6077 2010:6077 4005:6077 1011:6078 2010:6078 4005:6078 1012:6077 3001:6077 5001:6077 1012:6078 3001:6078 5001:6078 1013:6077 3002:6077 5002:6077 1013:6078 3002:6078 5002:6078

TABLE B Example combinations of a compound X with a compound Y. X:Y X:Y X:Y X:Y X:Y X:Y X:Y 6000:7000 6000:7001 6000:7002 6000:7003 6000:7004 6000:7005 6000:7006 6001:7000 6001:7001 6001:7002 6001:7003 6001:7004 6001:7005 6001:7006 6002:7000 6002:7001 6002:7002 6002:7003 6002:7004 6002:7005 6002:7006 6003:7000 6003:7001 6003:7002 6003:7003 6003:7004 6003:7005 6003:7006 6004:7000 6004:7001 6004:7002 6004:7003 6004:7004 6004:7005 6004:7006 6005:7000 6005:7001 6005:7002 6005:7003 6005:7004 6005:7005 6005:7006 6006:7000 6006:7001 6006:7002 6006:7003 6006:7004 6006:7005 6006:7006 6007:7000 6007:7001 6007:7002 6007:7003 6007:7004 6007:7005 6007:7006 6008:7000 6008:7001 6008:7002 6008:7003 6008:7004 6008:7005 6008:7006 6009:7000 6009:7001 6009:7002 6009:7003 6009:7004 6009:7005 6009:7006 6010:7000 6010:7001 6010:7002 6010:7003 6010:7004 6010:7005 6010:7006 6011:7000 6011:7001 6011:7002 6011:7003 6011:7004 6011:7005 6011:7006 6012:7000 6012:7001 6012:7002 6012:7003 6012:7004 6012:7005 6012:7006 6013:7000 6013:7001 6013:7002 6013:7003 6013:7004 6013:7005 6013:7006 6014:7000 6014:7001 6014:7002 6014:7003 6014:7004 6014:7005 6014:7006 6015:7000 6015:7001 6015:7002 6015:7003 6015:7004 6015:7005 6015:7006 6016:7000 6016:7001 6016:7002 6016:7003 6016:7004 6016:7005 6016:7006 6017:7000 6017:7001 6017:7002 6017:7003 6017:7004 6017:7005 6017:7006 6018:7000 6018:7001 6018:7002 6018:7003 6018:7004 6018:7005 6018:7006 6019:7000 6019:7001 6019:7002 6019:7003 6019:7004 6019:7005 6019:7006 6020:7000 6020:7001 6020:7002 6020:7003 6020:7004 6020:7005 6020:7006 6000:7007 6000:7008 6000:7009 6000:7010 6000:7011 6000:7012 6000:7013 6001:7007 6001:7008 6001:7009 6001:7010 6001:7011 6001:7012 6001:7013 6002:7007 6002:7008 6002:7009 6002:7010 6002:7011 6002:7012 6002:7013 6003:7007 6003:7008 6003:7009 6003:7010 6003:7011 6003:7012 6003:7013 6004:7007 6004:7008 6004:7009 6004:7010 6004:7011 6004:7012 6004:7013 6005:7007 6005:7008 6005:7009 6005:7010 6005:7011 6005:7012 6005:7013 6006:7007 6006:7008 6006:7009 6006:7010 6006:7011 6006:7012 6006:7013 6007:7007 6007:7008 6007:7009 6007:7010 6007:7011 6007:7012 6007:7013 6008:7007 6008:7008 6008:7009 6008:7010 6008:7011 6008:7012 6008:7013 6009:7007 6009:7008 6009:7009 6009:7010 6009:7011 6009:7012 6009:7013 6010:7007 6010:7008 6010:7009 6010:7010 6010:7011 6010:7012 6010:7013 6011:7007 6011:7008 6011:7009 6011:7010 6011:7011 6011:7012 6011:7013 6012:7007 6012:7008 6012:7009 6012:7010 6012:7011 6012:7012 6012:7013 6013:7007 6013:7008 6013:7009 6013:7010 6013:7011 6013:7012 6013:7013 6014:7007 6014:7008 6014:7009 6014:7010 6014:7011 6014:7012 6014:7013 6015:7007 6015:7008 6015:7009 6015:7010 6015:7011 6015:7012 6015:7013 6016:7007 6016:7008 6016:7009 6016:7010 6016:7011 6016:7012 6016:7013 6017:7007 6017:7008 6017:7009 6017:7010 6017:7011 6017:7012 6017:7013 6018:7007 6018:7008 6018:7009 6018:7010 6018:7011 6018:7012 6018:7013 6019:7007 6019:7008 6019:7009 6019:7010 6019:7011 6019:7012 6019:7013 6020:7007 6020:7008 6020:7009 6020:7010 6020:7011 6020:7012 6020:7013 6000:7014 6000:7015 6000:7016 6000:7017 6000:7018 6000:7019 6000:7020 6001:7014 6001:7015 6001:7016 6001:7017 6001:7018 6001:7019 6001:7020 6002:7014 6002:7015 6002:7016 6002:7017 6002:7018 6002:7019 6002:7020 6003:7014 6003:7015 6003:7016 6003:7017 6003:7018 6003:7019 6003:7020 6004:7014 6004:7015 6004:7016 6004:7017 6004:7018 6004:7019 6004:7020 6005:7014 6005:7015 6005:7016 6005:7017 6005:7018 6005:7019 6005:7020 6006:7014 6006:7015 6006:7016 6006:7017 6006:7018 6006:7019 6006:7020 6007:7014 6007:7015 6007:7016 6007:7017 6007:7018 6007:7019 6007:7020 6008:7014 6008:7015 6008:7016 6008:7017 6008:7018 6008:7019 6008:7020 6009:7014 6009:7015 6009:7016 6009:7017 6009:7018 6009:7019 6009:7020 6010:7014 6010:7015 6010:7016 6010:7017 6010:7018 6010:7019 6010:7020 6011:7014 6011:7015 6011:7016 6011:7017 6011:7018 6011:7019 6011:7020 6012:7014 6012:7015 6012:7016 6012:7017 6012:7018 6012:7019 6012:7020 6013:7014 6013:7015 6013:7016 6013:7017 6013:7018 6013:7019 6013:7020 6014:7014 6014:7015 6014:7016 6014:7017 6014:7018 6014:7019 6014:7020 6015:7014 6015:7015 6015:7016 6015:7017 6015:7018 6015:7019 6015:7020 6016:7014 6016:7015 6016:7016 6016:7017 6016:7018 6016:7019 6016:7020 6017:7014 6017:7015 6017:7016 6017:7017 6017:7018 6017:7019 6017:7020 6018:7014 6018:7015 6018:7016 6018:7017 6018:7018 6018:7019 6018:7020 6019:7014 6019:7015 6019:7016 6019:7017 6019:7018 6019:7019 6019:7020 6020:7014 6020:7015 6020:7016 6020:7017 6020:7018 6020:7019 6020:7020 6000:7021 6000:7022 6000:7023 6000:7024 6000:7025 6000:7026 6000:7027 6001:7021 6001:7022 6001:7023 6001:7024 6001:7025 6001:7026 6001:7027 6002:7021 6002:7022 6002:7023 6002:7024 6002:7025 6002:7026 6002:7027 6003:7021 6003:7022 6003:7023 6003:7024 6003:7025 6003:7026 6003:7027 6004:7021 6004:7022 6004:7023 6004:7024 6004:7025 6004:7026 6004:7027 6005:7021 6005:7022 6005:7023 6005:7024 6005:7025 6005:7026 6005:7027 6006:7021 6006:7022 6006:7023 6006:7024 6006:7025 6006:7026 6006:7027 6007:7021 6007:7022 6007:7023 6007:7024 6007:7025 6007:7026 6007:7027 6008:7021 6008:7022 6008:7023 6008:7024 6008:7025 6008:7026 6008:7027 6009:7021 6009:7022 6009:7023 6009:7024 6009:7025 6009:7026 6009:7027 6010:7021 6010:7022 6010:7023 6010:7024 6010:7025 6010:7026 6010:7027 6011:7021 6011:7022 6011:7023 6011:7024 6011:7025 6011:7026 6011:7027 6012:7021 6012:7022 6012:7023 6012:7024 6012:7025 6012:7026 6012:7027 6013:7021 6013:7022 6013:7023 6013:7024 6013:7025 6013:7026 6013:7027 6014:7021 6014:7022 6014:7023 6014:7024 6014:7025 6014:7026 6014:7027 6015:7021 6015:7022 6015:7023 6015:7024 6015:7025 6015:7026 6015:7027 6016:7021 6016:7022 6016:7023 6016:7024 6016:7025 6016:7026 6016:7027 6017:7021 6017:7022 6017:7023 6017:7024 6017:7025 6017:7026 6017:7027 6018:7021 6018:7022 6018:7023 6018:7024 6018:7025 6018:7026 6018:7027 6019:7021 6019:7022 6019:7023 6019:7024 6019:7025 6019:7026 6019:7027 6020:7021 6020:7022 6020:7023 6020:7024 6020:7025 6020:7026 6020:7027 6000:7028 6000:7029 6000:7030 6000:7031 6000:7032 6000:7033 6000:7034 6001:7028 6001:7029 6001:7030 6001:7031 6001:7032 6001:7033 6001:7034 6002:7028 6002:7029 6002:7030 6002:7031 6002:7032 6002:7033 6002:7034 6003:7028 6003:7029 6003:7030 6003:7031 6003:7032 6003:7033 6003:7034 6004:7028 6004:7029 6004:7030 6004:7031 6004:7032 6004:7033 6004:7034 6005:7028 6005:7029 6005:7030 6005:7031 6005:7032 6005:7033 6005:7034 6006:7028 6006:7029 6006:7030 6006:7031 6006:7032 6006:7033 6006:7034 6007:7028 6007:7029 6007:7030 6007:7031 6007:7032 6007:7033 6007:7034 6008:7028 6008:7029 6008:7030 6008:7031 6008:7032 6008:7033 6008:7034 6009:7028 6009:7029 6009:7030 6009:7031 6009:7032 6009:7033 6009:7034 6010:7028 6010:7029 6010:7030 6010:7031 6010:7032 6010:7033 6010:7034 6011:7028 6011:7029 6011:7030 6011:7031 6011:7032 6011:7033 6011:7034 6012:7028 6012:7029 6012:7030 6012:7031 6012:7032 6012:7033 6012:7034 6013:7028 6013:7029 6013:7030 6013:7031 6013:7032 6013:7033 6013:7034 6014:7028 6014:7029 6014:7030 6014:7031 6014:7032 6014:7033 6014:7034 6015:7028 6015:7029 6015:7030 6015:7031 6015:7032 6015:7033 6015:7034 6016:7028 6016:7029 6016:7030 6016:7031 6016:7032 6016:7033 6016:7034 6017:7028 6017:7029 6017:7030 6017:7031 6017:7032 6017:7033 6017:7034 6018:7028 6018:7029 6018:7030 6018:7031 6018:7032 6018:7033 6018:7034 6019:7028 6019:7029 6019:7030 6019:7031 6019:7032 6019:7033 6019:7034 6020:7028 6020:7029 6020:7030 6020:7031 6020:7032 6020:7033 6020:7034 6000:7035 6000:7036 6000:7037 6000:7038 6000:7039 6000:7040 6000:7041 6001:7035 6001:7036 6001:7037 6001:7038 6001:7039 6001:7040 6001:7041 6002:7035 6002:7036 6002:7037 6002:7038 6002:7039 6002:7040 6002:7041 6003:7035 6003:7036 6003:7037 6003:7038 6003:7039 6003:7040 6003:7041 6004:7035 6004:7036 6004:7037 6004:7038 6004:7039 6004:7040 6004:7041 6005:7035 6005:7036 6005:7037 6005:7038 6005:7039 6005:7040 6005:7041 6006:7035 6006:7036 6006:7037 6006:7038 6006:7039 6006:7040 6006:7041 6007:7035 6007:7036 6007:7037 6007:7038 6007:7039 6007:7040 6007:7041 6008:7035 6008:7036 6008:7037 6008:7038 6008:7039 6008:7040 6008:7041 6009:7035 6009:7036 6009:7037 6009:7038 6009:7039 6009:7040 6009:7041 6010:7035 6010:7036 6010:7037 6010:7038 6010:7039 6010:7040 6010:7041 6011:7035 6011:7036 6011:7037 6011:7038 6011:7039 6011:7040 6011:7041 6012:7035 6012:7036 6012:7037 6012:7038 6012:7039 6012:7040 6012:7041 6013:7035 6013:7036 6013:7037 6013:7038 6013:7039 6013:7040 6013:7041 6014:7035 6014:7036 6014:7037 6014:7038 6014:7039 6014:7040 6014:7041 6015:7035 6015:7036 6015:7037 6015:7038 6015:7039 6015:7040 6015:7041 6016:7035 6016:7036 6016:7037 6016:7038 6016:7039 6016:7040 6016:7041 6017:7035 6017:7036 6017:7037 6017:7038 6017:7039 6017:7040 6017:7041 6018:7035 6018:7036 6018:7037 6018:7038 6018:7039 6018:7040 6018:7041 6019:7035 6019:7036 6019:7037 6019:7038 6019:7039 6019:7040 6019:7041 6020:7035 6020:7036 6020:7037 6020:7038 6020:7039 6020:7040 6020:7041 6000:7042 6000:7043 6000:7044 6000:7045 6000:7046 6000:7047 6000:7048 6001:7042 6001:7043 6001:7044 6001:7045 6001:7046 6001:7047 6001:7048 6002:7042 6002:7043 6002:7044 6002:7045 6002:7046 6002:7047 6002:7048 6003:7042 6003:7043 6003:7044 6003:7045 6003:7046 6003:7047 6003:7048 6004:7042 6004:7043 6004:7044 6004:7045 6004:7046 6004:7047 6004:7048 6005:7042 6005:7043 6005:7044 6005:7045 6005:7046 6005:7047 6005:7048 6006:7042 6006:7043 6006:7044 6006:7045 6006:7046 6006:7047 6006:7048 6007:7042 6007:7043 6007:7044 6007:7045 6007:7046 6007:7047 6007:7048 6008:7042 6008:7043 6008:7044 6008:7045 6008:7046 6008:7047 6008:7048 6009:7042 6009:7043 6009:7044 6009:7045 6009:7046 6009:7047 6009:7048 6010:7042 6010:7043 6010:7044 6010:7045 6010:7046 6010:7047 6010:7048 6011:7042 6011:7043 6011:7044 6011:7045 6011:7046 6011:7047 6011:7048 6012:7042 6012:7043 6012:7044 6012:7045 6012:7046 6012:7047 6012:7048 6013:7042 6013:7043 6013:7044 6013:7045 6013:7046 6013:7047 6013:7048 6014:7042 6014:7043 6014:7044 6014:7045 6014:7046 6014:7047 6014:7048 6015:7042 6015:7043 6015:7044 6015:7045 6015:7046 6015:7047 6015:7048 6016:7042 6016:7043 6016:7044 6016:7045 6016:7046 6016:7047 6016:7048 6017:7042 6017:7043 6017:7044 6017:7045 6017:7046 6017:7047 6017:7048 6018:7042 6018:7043 6018:7044 6018:7045 6018:7046 6018:7047 6018:7048 6019:7042 6019:7043 6019:7044 6019:7045 6019:7046 6019:7047 6019:7048 6020:7042 6020:7043 6020:7044 6020:7045 6020:7046 6020:7047 6020:7048 6000:7049 6000:7050 6000:7051 6000:7052 6000:7053 6000:7054 6000:7055 6001:7049 6001:7050 6001:7051 6001:7052 6001:7053 6001:7054 6001:7055 6002:7049 6002:7050 6002:7051 6002:7052 6002:7053 6002:7054 6002:7055 6003:7049 6003:7050 6003:7051 6003:7052 6003:7053 6003:7054 6003:7055 6004:7049 6004:7050 6004:7051 6004:7052 6004:7053 6004:7054 6004:7055 6005:7049 6005:7050 6005:7051 6005:7052 6005:7053 6005:7054 6005:7055 6006:7049 6006:7050 6006:7051 6006:7052 6006:7053 6006:7054 6006:7055 6007:7049 6007:7050 6007:7051 6007:7052 6007:7053 6007:7054 6007:7055 6008:7049 6008:7050 6008:7051 6008:7052 6008:7053 6008:7054 6008:7055 6009:7049 6009:7050 6009:7051 6009:7052 6009:7053 6009:7054 6009:7055 6010:7049 6010:7050 6010:7051 6010:7052 6010:7053 6010:7054 6010:7055 6011:7049 6011:7050 6011:7051 6011:7052 6011:7053 6011:7054 6011:7055 6012:7049 6012:7050 6012:7051 6012:7052 6012:7053 6012:7054 6012:7055 6013:7049 6013:7050 6013:7051 6013:7052 6013:7053 6013:7054 6013:7055 6014:7049 6014:7050 6014:7051 6014:7052 6014:7053 6014:7054 6014:7055 6015:7049 6015:7050 6015:7051 6015:7052 6015:7053 6015:7054 6015:7055 6016:7049 6016:7050 6016:7051 6016:7052 6016:7053 6016:7054 6016:7055 6017:7049 6017:7050 6017:7051 6017:7052 6017:7053 6017:7054 6017:7055 6018:7049 6018:7050 6018:7051 6018:7052 6018:7053 6018:7054 6018:7055 6019:7049 6019:7050 6019:7051 6019:7052 6019:7053 6019:7054 6019:7055 6020:7049 6020:7050 6020:7051 6020:7052 6020:7053 6020:7054 6020:7055 6000:7056 6000:7057 6000:7058 6000:7059 6000:7060 6000:7061 6000:7062 6001:7056 6001:7057 6001:7058 6001:7059 6001:7060 6001:7061 6001:7062 6002:7056 6002:7057 6002:7058 6002:7059 6002:7060 6002:7061 6002:7062 6003:7056 6003:7057 6003:7058 6003:7059 6003:7060 6003:7061 6003:7062 6004:7056 6004:7057 6004:7058 6004:7059 6004:7060 6004:7061 6004:7062 6005:7056 6005:7057 6005:7058 6005:7059 6005:7060 6005:7061 6005:7062 6006:7056 6006:7057 6006:7058 6006:7059 6006:7060 6006:7061 6006:7062 6007:7056 6007:7057 6007:7058 6007:7059 6007:7060 6007:7061 6007:7062 6008:7056 6008:7057 6008:7058 6008:7059 6008:7060 6008:7061 6008:7062 6009:7056 6009:7057 6009:7058 6009:7059 6009:7060 6009:7061 6009:7062 6010:7056 6010:7057 6010:7058 6010:7059 6010:7060 6010:7061 6010:7062 6011:7056 6011:7057 6011:7058 6011:7059 6011:7060 6011:7061 6011:7062 6012:7056 6012:7057 6012:7058 6012:7059 6012:7060 6012:7061 6012:7062 6013:7056 6013:7057 6013:7058 6013:7059 6013:7060 6013:7061 6013:7062 6014:7056 6014:7057 6014:7058 6014:7059 6014:7060 6014:7061 6014:7062 6015:7056 6015:7057 6015:7058 6015:7059 6015:7060 6015:7061 6015:7062 6016:7056 6016:7057 6016:7058 6016:7059 6016:7060 6016:7061 6016:7062 6017:7056 6017:7057 6017:7058 6017:7059 6017:7060 6017:7061 6017:7062 6018:7056 6018:7057 6018:7058 6018:7059 6018:7060 6018:7061 6018:7062 6019:7056 6019:7057 6019:7058 6019:7059 6019:7060 6019:7061 6019:7062 6020:7056 6020:7057 6020:7058 6020:7059 6020:7060 6020:7061 6020:7062 6000:7063 6000:7064 6000:7065 6000:7066 6000:7067 6000:7068 6000:7069 6001:7063 6001:7064 6001:7065 6001:7066 6001:7067 6001:7068 6001:7069 6002:7063 6002:7064 6002:7065 6002:7066 6002:7067 6002:7068 6002:7069 6003:7063 6003:7064 6003:7065 6003:7066 6003:7067 6003:7068 6003:7069 6004:7063 6004:7064 6004:7065 6004:7066 6004:7067 6004:7068 6004:7069 6005:7063 6005:7064 6005:7065 6005:7066 6005:7067 6005:7068 6005:7069 6006:7063 6006:7064 6006:7065 6006:7066 6006:7067 6006:7068 6006:7069 6007:7063 6007:7064 6007:7065 6007:7066 6007:7067 6007:7068 6007:7069 6008:7063 6008:7064 6008:7065 6008:7066 6008:7067 6008:7068 6008:7069 6009:7063 6009:7064 6009:7065 6009:7066 6009:7067 6009:7068 6009:7069 6010:7063 6010:7064 6010:7065 6010:7066 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6073:7054 6073:7055 6073:7056 6073:7057 6073:7058 6073:7059 6074:7053 6074:7054 6074:7055 6074:7056 6074:7057 6074:7058 6074:7059 6075:7053 6075:7054 6075:7055 6075:7056 6075:7057 6075:7058 6075:7059 6076:7053 6076:7054 6076:7055 6076:7056 6076:7057 6076:7058 6076:7059 6077:7053 6077:7054 6077:7055 6077:7056 6077:7057 6077:7058 6077:7059 6078:7053 6078:7054 6078:7055 6078:7056 6078:7057 6078:7058 6078:7059 6061:7060 6061:7061 6061:7062 6061:7063 6061:7064 6061:7065 6061:7066 6062:7060 6062:7061 6062:7062 6062:7063 6062:7064 6062:7065 6062:7066 6063:7060 6063:7061 6063:7062 6063:7063 6063:7064 6063:7065 6063:7066 6064:7060 6064:7061 6064:7062 6064:7063 6064:7064 6064:7065 6064:7066 6065:7060 6065:7061 6065:7062 6065:7063 6065:7064 6065:7065 6065:7066 6066:7060 6066:7061 6066:7062 6066:7063 6066:7064 6066:7065 6066:7066 6067:7060 6067:7061 6067:7062 6067:7063 6067:7064 6067:7065 6067:7066 6068:7060 6068:7061 6068:7062 6068:7063 6068:7064 6068:7065 6068:7066 6069:7060 6069:7061 6069:7062 6069:7063 6069:7064 6069:7065 6069:7066 6070:7060 6070:7061 6070:7062 6070:7063 6070:7064 6070:7065 6070:7066 6071:7060 6071:7061 6071:7062 6071:7063 6071:7064 6071:7065 6071:7066 6072:7060 6072:7061 6072:7062 6072:7063 6072:7064 6072:7065 6072:7066 6073:7060 6073:7061 6073:7062 6073:7063 6073:7064 6073:7065 6073:7066 6074:7060 6074:7061 6074:7062 6074:7063 6074:7064 6074:7065 6074:7066 6075:7060 6075:7061 6075:7062 6075:7063 6075:7064 6075:7065 6075:7066 6076:7060 6076:7061 6076:7062 6076:7063 6076:7064 6076:7065 6076:7066 6077:7060 6077:7061 6077:7062 6077:7063 6077:7064 6077:7065 6077:7066 6078:7060 6078:7061 6078:7062 6078:7063 6078:7064 6078:7065 6078:7066 6061:7067 6061:7068 6061:7069 6061:7070 6061:7071 6061:7072 6061:7073 6062:7067 6062:7068 6062:7069 6062:7070 6062:7071 6062:7072 6062:7073 6063:7067 6063:7068 6063:7069 6063:7070 6063:7071 6063:7072 6063:7073 6064:7067 6064:7068 6064:7069 6064:7070 6064:7071 6064:7072 6064:7073 6065:7067 6065:7068 6065:7069 6065:7070 6065:7071 6065:7072 6065:7073 6066:7067 6066:7068 6066:7069 6066:7070 6066:7071 6066:7072 6066:7073 6067:7067 6067:7068 6067:7069 6067:7070 6067:7071 6067:7072 6067:7073 6068:7067 6068:7068 6068:7069 6068:7070 6068:7071 6068:7072 6068:7073 6069:7067 6069:7068 6069:7069 6069:7070 6069:7071 6069:7072 6069:7073 6070:7067 6070:7068 6070:7069 6070:7070 6070:7071 6070:7072 6070:7073 6071:7067 6071:7068 6071:7069 6071:7070 6071:7071 6071:7072 6071:7073 6072:7067 6072:7068 6072:7069 6072:7070 6072:7071 6072:7072 6072:7073 6073:7067 6073:7068 6073:7069 6073:7070 6073:7071 6073:7072 6073:7073 6074:7067 6074:7068 6074:7069 6074:7070 6074:7071 6074:7072 6074:7073 6075:7067 6075:7068 6075:7069 6075:7070 6075:7071 6075:7072 6075:7073 6076:7067 6076:7068 6076:7069 6076:7070 6076:7071 6076:7072 6076:7073 6077:7067 6077:7068 6077:7069 6077:7070 6077:7071 6077:7072 6077:7073 6078:7067 6078:7068 6078:7069 6078:7070 6078:7071 6078:7072 6078:7073 6061:7074 6061:7075 6061:7076 6061:7077 — — — 6062:7074 6062:7075 6062:7076 6062:7077 6063:7074 6063:7075 6063:7076 6063:7077 6064:7074 6064:7075 6064:7076 6064:7077 6065:7074 6065:7075 6065:7076 6065:7077 6066:7074 6066:7075 6066:7076 6066:7077 6067:7074 6067:7075 6067:7076 6067:7077 6068:7074 6068:7075 6068:7076 6068:7077 6069:7074 6069:7075 6069:7076 6069:7077 6070:7074 6070:7075 6070:7076 6070:7077 6071:7074 6071:7075 6071:7076 6071:7077 6072:7074 6072:7075 6072:7076 6072:7077 6073:7074 6073:7075 6073:7076 6073:7077 6074:7074 6074:7075 6074:7076 6074:7077 6075:7074 6075:7075 6075:7076 6075:7077 6076:7074 6076:7075 6076:7076 6076:7077 6077:7074 6077:7075 6077:7076 6077:7077 6078:7074 6078:7075 6078:7076 6078:7077

TABLE C Example combinations of a compound X with a compound Y. X:Y X:Y X:Y X:Y X:Y X:Y 6000:8000 6000:8001 6000:8002 6000:8003 6000:8004 6000:8005 6001:8000 6001:8001 6001:8002 6001:8003 6001:8004 6001:8005 6002:8000 6002:8001 6002:8002 6002:8003 6002:8004 6002:8005 6003:8000 6003:8001 6003:8002 6003:8003 6003:8004 6003:8005 6004:8000 6004:8001 6004:8002 6004:8003 6004:8004 6004:8005 6005:8000 6005:8001 6005:8002 6005:8003 6005:8004 6005:8005 6006:8000 6006:8001 6006:8002 6006:8003 6006:8004 6006:8005 6007:8000 6007:8001 6007:8002 6007:8003 6007:8004 6007:8005 6008:8000 6008:8001 6008:8002 6008:8003 6008:8004 6008:8005 6009:8000 6009:8001 6009:8002 6009:8003 6009:8004 6009:8005 6010:8000 6010:8001 6010:8002 6010:8003 6010:8004 6010:8005 6011:8000 6011:8001 6011:8002 6011:8003 6011:8004 6011:8005 6012:8000 6012:8001 6012:8002 6012:8003 6012:8004 6012:8005 6013:8000 6013:8001 6013:8002 6013:8003 6013:8004 6013:8005 6014:8000 6014:8001 6014:8002 6014:8003 6014:8004 6014:8005 6015:8000 6015:8001 6015:8002 6015:8003 6015:8004 6015:8005 6016:8000 6016:8001 6016:8002 6016:8003 6016:8004 6016:8005 6017:8000 6017:8001 6017:8002 6017:8003 6017:8004 6017:8005 6018:8000 6018:8001 6018:8002 6018:8003 6018:8004 6018:8005 6019:8000 6019:8001 6019:8002 6019:8003 6019:8004 6019:8005 6020:8000 6020:8001 6020:8002 6020:8003 6020:8004 6020:8005 6000:8006 6000:8007 6000:8008 6000:8009 6000:8010 6000:8011 6001:8006 6001:8007 6001:8008 6001:8009 6001:8010 6001:8011 6002:8006 6002:8007 6002:8008 6002:8009 6002:8010 6002:8011 6003:8006 6003:8007 6003:8008 6003:8009 6003:8010 6003:8011 6004:8006 6004:8007 6004:8008 6004:8009 6004:8010 6004:8011 6005:8006 6005:8007 6005:8008 6005:8009 6005:8010 6005:8011 6006:8006 6006:8007 6006:8008 6006:8009 6006:8010 6006:8011 6007:8006 6007:8007 6007:8008 6007:8009 6007:8010 6007:8011 6008:8006 6008:8007 6008:8008 6008:8009 6008:8010 6008:8011 6009:8006 6009:8007 6009:8008 6009:8009 6009:8010 6009:8011 6010:8006 6010:8007 6010:8008 6010:8009 6010:8010 6010:8011 6011:8006 6011:8007 6011:8008 6011:8009 6011:8010 6011:8011 6012:8006 6012:8007 6012:8008 6012:8009 6012:8010 6012:8011 6013:8006 6013:8007 6013:8008 6013:8009 6013:8010 6013:8011 6014:8006 6014:8007 6014:8008 6014:8009 6014:8010 6014:8011 6015:8006 6015:8007 6015:8008 6015:8009 6015:8010 6015:8011 6016:8006 6016:8007 6016:8008 6016:8009 6016:8010 6016:8011 6017:8006 6017:8007 6017:8008 6017:8009 6017:8010 6017:8011 6018:8006 6018:8007 6018:8008 6018:8009 6018:8010 6018:8011 6019:8006 6019:8007 6019:8008 6019:8009 6019:8010 6019:8011 6020:8006 6020:8007 6020:8008 6020:8009 6020:8010 6020:8011 6000:8012 6021:8000 6021:8001 6021:8002 6021:8003 6021:8004 6001:8012 6022:8000 6022:8001 6022:8002 6022:8003 6022:8004 6002:8012 6023:8000 6023:8001 6023:8002 6023:8003 6023:8004 6003:8012 6024:8000 6024:8001 6024:8002 6024:8003 6024:8004 6004:8012 6025:8000 6025:8001 6025:8002 6025:8003 6025:8004 6005:8012 6026:8000 6026:8001 6026:8002 6026:8003 6026:8004 6006:8012 6027:8000 6027:8001 6027:8002 6027:8003 6027:8004 6007:8012 6028:8000 6028:8001 6028:8002 6028:8003 6028:8004 6008:8012 6029:8000 6029:8001 6029:8002 6029:8003 6029:8004 6009:8012 6030:8000 6030:8001 6030:8002 6030:8003 6030:8004 6010:8012 6031:8000 6031:8001 6031:8002 6031:8003 6031:8004 6011:8012 6032:8000 6032:8001 6032:8002 6032:8003 6032:8004 6012:8012 6033:8000 6033:8001 6033:8002 6033:8003 6033:8004 6013:8012 6034:8000 6034:8001 6034:8002 6034:8003 6034:8004 6014:8012 6035:8000 6035:8001 6035:8002 6035:8003 6035:8004 6015:8012 6036:8000 6036:8001 6036:8002 6036:8003 6036:8004 6016:8012 6037:8000 6037:8001 6037:8002 6037:8003 6037:8004 6017:8012 6038:8000 6038:8001 6038:8002 6038:8003 6038:8004 6018:8012 6039:8000 6039:8001 6039:8002 6039:8003 6039:8004 6019:8012 6040:8000 6040:8001 6040:8002 6040:8003 6040:8004 6020:8012 6021:8005 6021:8006 6021:8007 6021:8008 6021:8009 6021:8010 6022:8005 6022:8006 6022:8007 6022:8008 6022:8009 6022:8010 6023:8005 6023:8006 6023:8007 6023:8008 6023:8009 6023:8010 6024:8005 6024:8006 6024:8007 6024:8008 6024:8009 6024:8010 6025:8005 6025:8006 6025:8007 6025:8008 6025:8009 6025:8010 6026:8005 6026:8006 6026:8007 6026:8008 6026:8009 6026:8010 6027:8005 6027:8006 6027:8007 6027:8008 6027:8009 6027:8010 6028:8005 6028:8006 6028:8007 6028:8008 6028:8009 6028:8010 6029:8005 6029:8006 6029:8007 6029:8008 6029:8009 6029:8010 6030:8005 6030:8006 6030:8007 6030:8008 6030:8009 6030:8010 6031:8005 6031:8006 6031:8007 6031:8008 6031:8009 6031:8010 6032:8005 6032:8006 6032:8007 6032:8008 6032:8009 6032:8010 6033:8005 6033:8006 6033:8007 6033:8008 6033:8009 6033:8010 6034:8005 6034:8006 6034:8007 6034:8008 6034:8009 6034:8010 6035:8005 6035:8006 6035:8007 6035:8008 6035:8009 6035:8010 6036:8005 6036:8006 6036:8007 6036:8008 6036:8009 6036:8010 6037:8005 6037:8006 6037:8007 6037:8008 6037:8009 6037:8010 6038:8005 6038:8006 6038:8007 6038:8008 6038:8009 6038:8010 6039:8005 6039:8006 6039:8007 6039:8008 6039:8009 6039:8010 6040:8005 6040:8006 6040:8007 6040:8008 6040:8009 6040:8010 6021:8011 6021:8012 6041:8000 6041:8001 6041:8002 6041:8003 6022:8011 6022:8012 6042:8000 6042:8001 6042:8002 6042:8003 6023:8011 6023:8012 6043:8000 6043:8001 6043:8002 6043:8003 6024:8011 6024:8012 6044:8000 6044:8001 6044:8002 6044:8003 6025:8011 6025:8012 6045:8000 6045:8001 6045:8002 6045:8003 6026:8011 6026:8012 6046:8000 6046:8001 6046:8002 6046:8003 6027:8011 6027:8012 6047:8000 6047:8001 6047:8002 6047:8003 6028:8011 6028:8012 6048:8000 6048:8001 6048:8002 6048:8003 6029:8011 6029:8012 6049:8000 6049:8001 6049:8002 6049:8003 6030:8011 6030:8012 6050:8000 6050:8001 6050:8002 6050:8003 6031:8011 6031:8012 6051:8000 6051:8001 6051:8002 6051:8003 6032:8011 6032:8012 6052:8000 6052:8001 6052:8002 6052:8003 6033:8011 6033:8012 6053:8000 6053:8001 6053:8002 6053:8003 6034:8011 6034:8012 6054:8000 6054:8001 6054:8002 6054:8003 6035:8011 6035:8012 6055:8000 6055:8001 6055:8002 6055:8003 6036:8011 6036:8012 6056:8000 6056:8001 6056:8002 6056:8003 6037:8011 6037:8012 6057:8000 6057:8001 6057:8002 6057:8003 6038:8011 6038:8012 6058:8000 6058:8001 6058:8002 6058:8003 6039:8011 6039:8012 6059:8000 6059:8001 6059:8002 6059:8003 6040:8011 6040:8012 6060:8000 6060:8001 6060:8002 6060:8003 6041:8004 6041:8005 6041:8006 6041:8007 6041:8008 6041:8009 6042:8004 6042:8005 6042:8006 6042:8007 6042:8008 6042:8009 6043:8004 6043:8005 6043:8006 6043:8007 6043:8008 6043:8009 6044:8004 6044:8005 6044:8006 6044:8007 6044:8008 6044:8009 6045:8004 6045:8005 6045:8006 6045:8007 6045:8008 6045:8009 6046:8004 6046:8005 6046:8006 6046:8007 6046:8008 6046:8009 6047:8004 6047:8005 6047:8006 6047:8007 6047:8008 6047:8009 6048:8004 6048:8005 6048:8006 6048:8007 6048:8008 6048:8009 6049:8004 6049:8005 6049:8006 6049:8007 6049:8008 6049:8009 6050:8004 6050:8005 6050:8006 6050:8007 6050:8008 6050:8009 6051:8004 6051:8005 6051:8006 6051:8007 6051:8008 6051:8009 6052:8004 6052:8005 6052:8006 6052:8007 6052:8008 6052:8009 6053:8004 6053:8005 6053:8006 6053:8007 6053:8008 6053:8009 6054:8004 6054:8005 6054:8006 6054:8007 6054:8008 6054:8009 6055:8004 6055:8005 6055:8006 6055:8007 6055:8008 6055:8009 6056:8004 6056:8005 6056:8006 6056:8007 6056:8008 6056:8009 6057:8004 6057:8005 6057:8006 6057:8007 6057:8008 6057:8009 6058:8004 6058:8005 6058:8006 6058:8007 6058:8008 6058:8009 6059:8004 6059:8005 6059:8006 6059:8007 6059:8008 6059:8009 6060:8004 6060:8005 6060:8006 6060:8007 6060:8008 6060:8009 6041:8010 6041:8011 6041:8012 6061:8000 6061:8001 6061:8002 6042:8010 6042:8011 6042:8012 6062:8000 6062:8001 6062:8002 6043:8010 6043:8011 6043:8012 6063:8000 6063:8001 6063:8002 6044:8010 6044:8011 6044:8012 6064:8000 6064:8001 6064:8002 6045:8010 6045:8011 6045:8012 6065:8000 6065:8001 6065:8002 6046:8010 6046:8011 6046:8012 6066:8000 6066:8001 6066:8002 6047:8010 6047:8011 6047:8012 6067:8000 6067:8001 6067:8002 6048:8010 6048:8011 6048:8012 6068:8000 6068:8001 6068:8002 6049:8010 6049:8011 6049:8012 6069:8000 6069:8001 6069:8002 6050:8010 6050:8011 6050:8012 6070:8000 6070:8001 6070:8002 6051:8010 6051:8011 6051:8012 6071:8000 6071:8001 6071:8002 6052:8010 6052:8011 6052:8012 6072:8000 6072:8001 6072:8002 6053:8010 6053:8011 6053:8012 6073:8000 6073:8001 6073:8002 6054:8010 6054:8011 6054:8012 6074:8000 6074:8001 6074:8002 6055:8010 6055:8011 6055:8012 6075:8000 6075:8001 6075:8002 6056:8010 6056:8011 6056:8012 6076:8000 6076:8001 6076:8002 6057:8010 6057:8011 6057:8012 6077:8000 6077:8001 6077:8002 6058:8010 6058:8011 6058:8012 6078:8000 6078:8001 6078:8002 6059:8010 6059:8011 6059:8012 6060:8010 6060:8011 6060:8012 6061:8003 6061:8004 6061:8005 6061:8006 6061:8007 6061:8008 6062:8003 6062:8004 6062:8005 6062:8006 6062:8007 6062:8008 6063:8003 6063:8004 6063:8005 6063:8006 6063:8007 6063:8008 6064:8003 6064:8004 6064:8005 6064:8006 6064:8007 6064:8008 6065:8003 6065:8004 6065:8005 6065:8006 6065:8007 6065:8008 6066:8003 6066:8004 6066:8005 6066:8006 6066:8007 6066:8008 6067:8003 6067:8004 6067:8005 6067:8006 6067:8007 6067:8008 6068:8003 6068:8004 6068:8005 6068:8006 6068:8007 6068:8008 6069:8003 6069:8004 6069:8005 6069:8006 6069:8007 6069:8008 6070:8003 6070:8004 6070:8005 6070:8006 6070:8007 6070:8008 6071:8003 6071:8004 6071:8005 6071:8006 6071:8007 6071:8008 6072:8003 6072:8004 6072:8005 6072:8006 6072:8007 6072:8008 6073:8003 6073:8004 6073:8005 6073:8006 6073:8007 6073:8008 6074:8003 6074:8004 6074:8005 6074:8006 6074:8007 6074:8008 6075:8003 6075:8004 6075:8005 6075:8006 6075:8007 6075:8008 6076:8003 6076:8004 6076:8005 6076:8006 6076:8007 6076:8008 6077:8003 6077:8004 6077:8005 6077:8006 6077:8007 6077:8008 6078:8003 6078:8004 6078:8005 6078:8006 6078:8007 6078:8008 6061:8009 6061:8010 6061:8011 6061:8012 — — 6062:8009 6062:8010 6062:8011 6062:8012 6063:8009 6063:8010 6063:8011 6063:8012 6064:8009 6064:8010 6064:8011 6064:8012 6065:8009 6065:8010 6065:8011 6065:8012 6066:8009 6066:8010 6066:8011 6066:8012 6067:8009 6067:8010 6067:8011 6067:8012 6068:8009 6068:8010 6068:8011 6068:8012 6069:8009 6069:8010 6069:8011 6069:8012 6070:8009 6070:8010 6070:8011 6070:8012 6071:8009 6071:8010 6071:8011 6071:8012 6072:8009 6072:8010 6072:8011 6072:8012 6073:8009 6073:8010 6073:8011 6073:8012 6074:8009 6074:8010 6074:8011 6074:8012 6075:8009 6075:8010 6075:8011 6075:8012 6076:8009 6076:8010 6076:8011 6076:8012 6077:8009 6077:8010 6077:8011 6077:8012 6078:8009 6078:8010 6078:8011 6078:8012

TABLE D Example combinations of a compound X with a compound Y. X:Y X:Y X:Y X:Y 6000:9000 6020:9000 6040:9000 6060:9000 6001:9000 6021:9000 6041:9000 6061:9000 6002:9000 6022:9000 6042:9000 6062:9000 6003:9000 6023:9000 6043:9000 6063:9000 6004:9000 6024:9000 6044:9000 6064:9000 6005:9000 6025:9000 6045:9000 6065:9000 6006:9000 6026:9000 6046:9000 6066:9000 6007:9000 6027:9000 6047:9000 6067:9000 6008:9000 6028:9000 6048:9000 6068:9000 6009:9000 6029:9000 6049:9000 6069:9000 6010:9000 6030:9000 6050:9000 6070:9000 6011:9000 6031:9000 6051:9000 6071:9000 6012:9000 6032:9000 6052:9000 6072:9000 6013:9000 6033:9000 6053:9000 6073:9000 6014:9000 6034:9000 6054:9000 6074:9000 6015:9000 6035:9000 6055:9000 6075:9000 6016:9000 6036:9000 6056:9000 6076:9000 6017:9000 6037:9000 6057:9000 6077:9000 6018:9000 6038:9000 6058:9000 6078:9000 6019:9000 6039:9000 6059:9000

EXAMPLES

Additional embodiments are disclosed in further detail in the following examples, which are not in any way intended to limit the scope of the claims.

Example 1 General Synthesis of Reagents 1 and 2

Step 1: Synthesis of 1-naphthyloxydichlorophosphothioate reagent (1a)

A 500 mL round bottom flask containing a magnetic stir bar was charged with phosphorus thiotrichloride (5.7 g, 33.65 mmol) and 1-naphthol (4.85 g, 33.64 mmol), and 40 mL of diethyl ether was added. Under an argon atmosphere, the solution was cooled in a dry ice/acetone bath. After 10 minutes of cooling, triethylamine (4.7 mL, 33.7 mmol) was added, and a precipitate formed. The mixture was allowed to warm to ambient temperature, and was then stirred for 2 days. The precipitated triethylammonium hydrochloride was filtered off, and was washed twice with ether. The solvents were removed under reduced pressure to leave 9.8 g of compound 1a as a cloudy, light yellow oil. 1a was used in the next step without further purification.

Step 2: Synthesis of the L-alanine methyl ester derived 1-naphthyloxy-chlorophosphothioate reagent (2a)

Into a 250 mL round bottom flask containing 1-naphthol-dichlorophosphothioate reagent 1a (1.97 g, 7.1 mmol) and L-alanine methyl ester hydrochloride (0.99 g, 7.1 mmol) was added in 50 mL of dichloromethane. At water/ice temperature under an argon atmosphere, triethylamine (1 mL, 7.2 mmol) was added. The reaction was allowed to warm to ambient temperature and was then stirred overnight. The solvents were removed using a rotary evaporator. The residue was purified using chromatography on silica gel, and eluting with 20% ethyl acetate in hexanes. The product 2a (1.0 g) was obtained as a viscous oil. ³¹P NMR (CDCl₃, 64.78, 65.0) (approximately a 1:1 mixture of diastereomers).

The reagents shown in Tables 6 and 7 were prepared using the procedures described for compounds 1a and 2a, with the ArOH compounds listed in Table 6 in place of 1-naphthol, and with hydrochloride salts of the amino acids listed in Table 7 in place of L-alanine methyl ester hydrochloride.

TABLE 6 ArOH Dichloridates Reagent No. Phenol

1b p-fluoro-phenol

1c p-chloro-phenol

1d o-chloro-phenol

1e p-chloro-m- chloro-phenol

1f p-methyl-phenol

1g o-methyl-phenol

1h p-methoxy-phenol

1i quinolin-5-ol

1j pyridine-3-ol

1k

TABLE 7 Amino Aryloxy amino acid Reagent ³¹P NMR Acid thiophosphochloridate No. (CDCl₃) L-alanine isopropyl ester

2b 64.75 (s) 64.65 (s) L-alanine cyclohexyl ester

2c 64.80 (s) 64.69 (s) L-alanine neopentyl ester

2d 64.59 (s) 64.31 (s) L-alanine isopropyl ester

2e 64.51 (s) 64.23 (s) L-alanine cyclohexyl ester

2f 64.55 (s) 64.25 (s) L-alanine neopentyl ester

2g 64.51 (s) 64.27 (s) L-valine isopropyl ester

2h 67.72 65.87

Example 2 Preparation of 2′-C-Methyluridine 5′-(O-(1-naphthyl)-N—(S)-1-(methoxycarbonyl)ethyl)thiophosphoramidate (3a)

A solution of cyclopentylidine protected 2′-C-methyluridine (262 mg, 0.81 mmol) in 2 mL tetrahydrofuran was cooled in an ice/water bath under argon, and treated with 2.1 mL tBuMgCl (1 M, 2.1 mmol). After 10 minutes, reagent 2a (0.83 g, 2.4 mmol) was added as a solution in 2 mL of tetrahydrofuran (THF). The reaction was stirred at ambient temperature for 2 days. An additional 1 mL tBuMgCl was then added (1 mmol). After an additional 2 days, the reaction was diluted with ethyl acetate and water. The organic layer was washed two times with brine, and dried over sodium sulfate. Chromatography on silica gel using a gradient of 1% methanol in dichloromethane to 10% methanol in dichloromethane afforded 0.2 g of a residue which was used without further purification. To the residue was added 4 mL of 80% aqueous formic acid. The mixture was heated to 50° C. using a water bath. After 2 hours, the reaction was cooled, and the solvents were removed under reduced pressure. A solution of 1:1 methanol:toluene was added to the residue. The solvents were then removed under reduced pressure. The addition of a solution of 1:1 methanol:toluene and removal of solvents were repeated 2 more times. The product was isolated following chromatography using silica gel with a gradient from 4% to 8% methanol in dichloromethane. The solvent was removed, and the residue was taken up in chloroform and treated with excess hexanes. The supernatant was decanted off, and the remaining solid was subjected to high vacuum overnight. Product 3a was isolated as a colorless solid (22.2 mg). ³¹P NMR (CDCl₃, 67.12, 67.86) and mass spectral data (M−H⁻, 564.5) were consistent with the desired product 3a as a near 1:1 mixture of diastereomers at the phosphorus chiral center.

Example 3 Preparation of 2′-C-methyluridine 5′-(O-phenyl-N—(S)-1-(isopropoxycarbonyl)ethyl)thiophosphoramidate (3b)

Step 1: Compound 3b-1—

To a suspension of 2′-methyluridine (20 g, 77.52 mmol) in dry CH₃CN (200 mL) were added cyclopentanone (20 mL) and trimethylorthoformate (20 mL) followed by p-toluenesulfonic acid monohydrate (7.4 g, 38.76 mmol). The reaction mixture was stirred at 40° C. overnight. The solvent was evaporated. The residue was dissolved in ethyl acetate and washed with brine. The organic layer was dried and evaporated to give pure 3b-1 as a white solid (14.5 g, 57.7%). ¹H NMR (CDCl₃, 400 MHz) δ8.86 (s, 1H), 7.67 (d, J=8.0 Hz, 1H), 6.06 (s, 1H), 5.73 (d, J=8.0 Hz, 1H), 4.50 (d, J=4.8 Hz, 1H), 4.21 (m, 1H), 4.02-3.86 (m, 2H), 2.17 (m, 1H), 1.98, 1.83, 1.68 (m, 8H), 1.30 (s, 3H).

Step 2: Compound 3b-2—

To a suspension of 3b-1 (20 g, 61.7 mmol) in dry CH₃CN (100 mL) was added N-methylimidazole (50 mL) and 2b (80 g, 249.2 mmol). The reaction mixture was stirred at 70° C. for 2 h. Solvent was removed and the residue was dissolved in ethyl acetate (500 mL). The solution was washed with brine, dried and evaporated. The residue was purified on a silica gel column (20˜50% ethylacetate (EA) in petroleum ether (PE)) to give 3b-2 as a white foam (two isomers, 12.5 g, 33%). ¹H NMR (CDCl₃, 400 MHz) δ8.79-8.92 (m, 1H), 7.55 (m, 1H), 7.34 (m, 2H), 7.20 (m, 3H), 6.09 (d, J=13.6 Hz, 1H), 5.70-5.61 (m, 1H), 5.06-5.01 (m, 1H), 4.38-4.09 (m, 6H), 2.08 (m, 1H), 1.96 (m, 1H), 1.73 (m, 2H), 1.66 (m, 5H), 1.39 (m, 3H), 1.23 (m, 9H); ³¹P NMR (CDCl₃, 162 MHz) δ67.62, 67.31.

Step 3: Compound 3b—

Compound 3b-2 (10 g, 16.4 mmol) was suspended in 100 mL of 80% formic acid and the reaction mixture was stirred at 50° C. for 1.5 hours. Solvent was evaporated and the residue was co-evaporated with toluene to remove traces of acid and water. The residue was purified by RP HPLC (0.5% HCOOH in MeCN and water as mobile phase) to give 3b (a mixture of two P-diastereomers, 5.6 g, 63%). ¹H NMR (CD₃OD, 400 MHz) δ 7.79, 7.87 (2d, J=8.0 Hz, 1H), 7.18-7.38 (m, 5H), 5.98, 6.01 (2s, 1H), 5.59, 5.63 (2d, J=8.0 Hz, 1H), 4.95-5.05 (m, 1H), 4.51-4.56 (m, 1H), 4.30-4.44 (m, 1H), 4.05-4.17 (m, 2H), 3.82-3.87 (m, 1H), 1.34, 1.38 (2d, J=7.2 Hz, 3H), 1.17, 1.25 (2d, J=6.0 Hz, 6H), 1.24, 125 (2s, 3H); ³¹P NMR (CD₃OD, 162 MHz) δ68.17, 68.40; ESI-LCMS: m/z 544.0 [M+H]⁺.

Step 4: Separation of 3b(i)-Rp and 3b(ii)-Sp—

Compound 3b was separated into its Rp and Sp diastereomers by two methods: (a) supercritical fluid chromatography (SFC) and (b) crystallization.

(a) Via SFC:

Compound 3b (440 mg, consisting of both 3b(i)-Rp and 3b(ii)-Sp in ˜1:1 ratio) was subjected to separation by SFC (chiral PAK AD, 5 um. 250*30 mm using 25% MeOH and 75% CO₂ as mobile phase) to give 3b(i)-Rp (123.8 mg) and 3b(ii)-Sp (162.5 mg) as a white solid; 3b(i)-Rp: ¹H NMR (CD₃OD, 400 MHz) δ7.87 (d, J=8.4 Hz, 1H), 7.36 (t, J=8.0 Hz, 2H), 7.28 (d, J=8.8 Hz, 2H), 7.19 (t, J=7.6 Hz, 1H), 6.01 (s, 1H), 5.62 (d, J=8.0 Hz, 1H), 5.03-4.97 (m, 1H), 4.56-4.92 (m, 1H), 4.44-4.39 (m, 1H), 4.16-4.13 (m, 1H), 4.10-4.05 (m, 1H), 3.86 (d, J=9.2 Hz, 1H), 1.34 (d, J=7.2 Hz, 3H), 1.25 (d, J=6.4 Hz, 6H), 1.16 (s, 3H); ³¹P NMR (CD₃OD, 162 MHz) δ68.18; ESI-LCMS: m/z=544 [M+H]⁺. 3b(ii)-Sp: ¹H NMR (CD₃OD, 400 MHz) δ7.89 (d, J=8.0 Hz, 1H), 7.36 (t, J=8.0 Hz, 2H), 7.30 (d, J=8.4 Hz, 2H), 7.20 (t, J=8.0 Hz, 1H), 5.99 (s, 1H), 5.60 (d, J=8.4 Hz, 1H), 5.03-4.97 (m, 1H), 4.56-4.51 (m, 1H), 4.35-4.30 (m, 1H), 4.14-4.10 (m, 2H), 3.83 (d, J=9.2 Hz, 1H), 1.39 (d, J=7.2 Hz, 3H), 1.25 (d, J=6.4 Hz, 6H), 1.17 (s, 3H); ³¹P NMR (CD₃OD, 162 MHz) δ68.42; ESI-LCMS: m/z=566 [M+Na]⁺.

(b) Via Crystallization:

Compound 3b as a mixture of diastereomers (1:1, 10 g) was dissolved in 100 mL of dichloromethane (DCM)/ether (1:3). Hexane was added dropwise until the solution became cloudy. The solution was left at (room temperature) RT for 5 h and overnight at −20° C. Precipitated crystals were recrystallized from DCM/ether 1:3 v/v, and one more time from DCM/ether 1:2. Compound 3b(i)-Rp (3 g) was obtained as a pure single diastereomer. The mother liquor after first crystallization was concentrated, and then dissolved in isopropanol. Hexane was added (30% by volume). The clear solution was left overnight at RT to produce a small amount of crystals, which were used as seeds. The mother liquor was evaporated and crystallized 2 times from hexane/isopropanol (4:1) to give 2.3 g of 3b(ii)-Sp.

Example 4 Preparation of 2′,3′-O-dipropionyl-2′-C-methyluridine 5′-(O-phenyl-N—(S)-1-(isopropoxycarbonyl)ethyl)thiophosphoramidate (4a)

Compound 3b (85 mg, 0.156 mmol) was dissolved in 3 mL of dry pyridine. Propionic anhydride (0.1 mL, 0.624 mmol) was added, and the mixture left for 18 hours at ambient temperature. Water (7 mL) and ethyl acetate (7 mL) were added. The organic phase was separated, and the aqueous phase was extracted with ethyl acetate (2×5 mL). The combined organic extracts were washed with water, brine, dried over Na₂SO₄, and evaporated. The resulting oil was purified by flash chromatography using a gradient of methanol in dichloromethane from 0 to 4%. The fractions containing phosphorothioate were combined and concentrated in vacuum. Repurification by RP HPLC using a gradient of methanol in water from 50% to 100% yielded 44 mg of product 4a. ³¹P NMR (CDCl₃, 67.71, 67.74) and mass spectral analysis (M−H⁻, 654.5) were consistent with the desired product 4a as near 1:1 mixture of diastereomers at the phosphorus chiral center.

Example 5 Preparation of 2′-deoxy-2′-α-fluoro-2′-β-C-methyluridine 5′-(O-phenyl-N—(S)-1-(isopropoxycarbonyl)ethyl)thiophosphoramidate (3c)

2′-Deoxy-2′-fluoro-2′-methyluridine (200 mg, 0.62 mmol) was suspended in dry THF (20 mL) under N₂. A solution of 2b in dry THF (3 mL, 3 mmol), DMAP (4-dimethylaminopyridine) (100 mg, 0.9 mmol) and triethylamine (1 mL, 7 mmol) were added at RT. The reaction was stirred at 80° C. for 18 hrs. The solvents were removed, and the residue was purified by column and RP HPLC (HCOOH system) to give 3c as a white solid (3.5 mg). ¹H NMR (CDCl₃) δ8.49, 8.31 (m, 1H), 7.49, 7.43 (2d, J=8.0 Hz, 1H), 7.31, 7.26 (m, 2H), 7.19, 7.11 (m, 3H), 6.17, 6.11 (2d, J=7.2 Hz, 1H), 5.62, 5.53 (2d, 1H), 4.99, 4.93 (m, 1H), 4.54, 4.27 (m, 2H), 4.08, 4.02 (m, 3H), 3.89, 3.83 (m, 1H), 1.36, 1.22 (m, 6H), 1.20, 1.12 (m, 6H). ³¹P NMR (CDCl₃) δ68.08, 67.05. LCMS m/z 545.8 (MH⁺).

Example 6 Preparation of 2′-deoxy-2′-α-fluoro-2′-β-C-methyluridine 5′-(O-phenyl-N—(S)-1-(cyclohexoxycarbonyl)ethyl)thiophosphoramidate (3d)

Compound 3d was prepared using the procedure for preparing compound 3c, with 2c in place of 2b. ¹H NMR (DMSO-d₆) δ11.55 (s, 1H), 7.61 (d, J=8.4 Hz, 0.43H), 7.57 (d, J=7.6 Hz, 0.56H), 7.40 (m, 2H), 7.21 (overlap, 3H), 6.68 (m, 1H), 6.04 (m, 1H), 5.95 (d, J=7.6 Hz, 0.40H), 5.88 (d, J=6.8 Hz, 0.60H), 5.57 (s, 0.50H), 5.55 (s, 0.50H), 4.64 (s, 1H), 4.39 (m, 1H), 4.23 (m, 1H), 4.09-3.86 (m, 2H), 3.84 (m, 1H), 1.63 (s, 2H), 1.45 (s, 2H), 1.36 (brs, 1H), 1.34-1.29 (m, 11H). ³¹P NMR (DMSO-d₆) δ67.96, 67.89; MS m/z 586.2 (MH⁺).

Example 7 Preparation of 2′-deoxy-2′-α-fluoro-2′-β-C-methyluridine 5′-(O-phenyl-N—(S)-1-(neopentoxycarbonyl)ethyl)thiophosphoramidate (3e)

Compound 3e was prepared using the procedure for preparing compound 3c, with 2d in place of 2b. ¹H NMR (CD₃OD) δ7.77-7.66 (q, J=8.0, 8.4 Hz, 1H), 7.36-7.16 (m, 5H), 6.13 (m, 1H), 6.04 (m, 1H), 5.65-5.56 (q, J=8.4, 8.0 Hz, 1H), 4.19-4.09 (m, 2H), 3.93-3.75 (m, 2H), 1.41-1.28 (m, 6H), 0.93 (s, 9H). ³¹P NMR (CD₃OD) δ66.9, 66.9. MS m/z 574.2 (MH⁺).

Example 8 Preparation of 2′-C-methyluridine 5′-(O-phenyl-N—(S)-1-(neopentoxycarbonyl)ethyl)thiophosphoramidate (3f)

2′-C-methyluridine (77 mg, 0.3 mmol) was dissolved in 10 mL of anhydrous acetonitrile and 2 mL of N-methylimidazole. Compound 2d was added (0.3 g, 0.9 mmol) and the mixture was heated at 70° C. for 2 h. The solvent was removed under reduced pressure. The residue was dissolved in 30 mL of ethyl acetate, washed with 10% citric acid (2×10 mL), water, brine, dried over Na₂SO₄, and concentrated. The crude product was purified by flash chromatography on silica gel with methanol in dichloromethane (0 to 10%) to give 3f (224 mg) as light-tan solid. An analytical sample was obtained as a colorless solid by RP HPLC purification in gradient of methanol in water from 10% to 95% on a Synergy 4u Hydro-RP column (Phenominex). ¹H NMR (CDCl₃): δ 9.90 (bs, 1H), 7.62-7.58 (m, 1H), 7.32-7.28 (m, 2H), 7.20-7.16 (m, 2H), 5.97 & 5.94 (2s, 1H), 5.65 & 5.52 (2d, 1H), 4.54-4.46 (m, 1H), 4.39-4.24 (m, 1H), 4.20-4.04 (m, 3H), 3.85-3.79 (m, 1H), 3.73-3.65 (m, 2H), 1.39-1.32 (dd, 3H), 1.16-1.14 (d, 1H), 0.87-0.86 (m, 9H); ³¹P NMR: δ67.85, 67.16 (1:1 mixture of diastereomers); ESI-LCMS: m/z 570.4 [M+H]⁺.

Example 9 Preparation of 2′-C-Methyluridine 5′-(O-phenyl-N—(S)-1-(cyclohexoxycarbonyl)ethyl)thiophosphoramidate (3g)

Compound 3g was prepared using the procedure for preparing compound 3f, with 2c in place of 2d. ¹H NMR (CDCl₃): δ 9.40 (bs, 1H), 7.60-7.55 (m, 1H), 7.29-7.11 (m, 5H), 5.95 & 5.92 (2s, 1H), 5.63 & 5.53 (2d, 1H), 4.75-4.68 (m, 1H), 4.50-4.23 (m, 2H), 4.10-4.00 (m, 3H), 3.74-3.72 (m, 1H), 1.80-1.05 (m, 17H); ³¹P NMR: δ67.80, 67.16 (3:4 mixture of diastereomers); ESI-LCMS: m/z 582.5 [M+H]⁺.

Example 10 Preparation of 2′-C-Methyluridine 5′-(O-(1-naphthyl)-N—(S)-1-(isopropoxycarbonyl)ethyl)thiophosphoramidate (3h)

Compound 3h was prepared using the procedure for preparing compound 3f, with 2e in place of 2d. ¹H NMR (CDCl₃): δ 9.10 (bs, 1H), 8.05-7.20 (m, 9H), 5.95&5.92 (2s, 1H), 5.38 & 5.33 (2d, 1H), 4.99-4.91 (m, 1H), 4.59-4.28 (m, 2H), 4.20-4.03 (m, 3H), 3.72-3.69 (m, 1H), 1.36-1.27 (2d, 3H), 1.20-1.11 (m, 6H), 1.06-1.04 (2s, 3H); ³¹P NMR: δ 67.92, 67.28 (2:3 mixture of diastereomers); ESI-LCMS: m/z 592.2 [M+H]⁺.

Example 11 Preparation of 2′-C-Methyluridine 5′-(O-(1-naphthyl)-N—(S)-1-(cyclohexoxycarbonyl)ethyl)thiophosphoramidate (3i)

Compound 3i was prepared using the procedure for preparing compound 3f, with 2f in place of 2d. ¹H NMR (CDCl₃): δ 9.80 (bs, 1H), 8.05-7.30 (m, 9H), 5.92 & 5.91 (2s, 1H), 5.38-5.29 (2d, 1H), 4.79-4.69 (m, 1H), 4.59-4.32 (m, 1H), 4.50-4.46 (m, 1H), 4.38-4.03 (m, 4H), 3.70-3.66 (m, 1H), 1.80-1.00 (m, 17H); ³¹P NMR: δ67.74, 67.43 (1:1 mixture of diastereomers); ESI-LCMS: m/z 632.5 [M+H]⁺.

Example 12 Preparation of 2′-C-Methyluridine 5′-(O-(1-naphtyl)-N—(S)-1-(neopentoxycarbonyl)ethyl)thiophosphoramidate (3i)

Compound 3j was prepared using the procedure for preparing compound 3f, with 2g in place of 2d. ¹H NMR (CDCl₃): δ 9.80 (bs, 1H), 8.05-7.30 (m, 9H), 5.90 & 5.87 (2s, 1H), 5.38 &5.30 (2d, 1H), 4.60-3.60 (m, 9H), 3.72-3.69 (m, 1H), 1.41 & 1.39 (2d, 3H), 1.08 & 1.06 (2s, 3H), 0.87 & 0.86 (2s, 9H); ³¹P NMR: δ68.01, 67.35 (1:1 mixture of diastereomers); ESI-LCMS: m/z 620.8 [M+H]⁺.

Example 13 Preparation of 5′-dideuterated 2′-C-methyluridine 5′-(O-phenyl-N—(S)-1-(isopropoxycarbonyl)ethyl)thiophosphoramidate (3l)

Step 1. Compound 3l-1—

To a suspension of 2′-C-methyluridine (2.50 g, 7.6 mmol) in acetone (100 mL) were added p-Toluenesulfonic acid monohydrate (1.76 g, 9.2 mmol) and 2,2-dimethoxypropane (20 mL). The mixture was stirred at RT for 16 h. Then saturated NaHCO₃ was added to adjust the pH to between approximately 6-7. The suspension was concentrated and the residue was purified on a silica gel column (5-7% MeOH in DCM) to give 3l-1 as a white solid (2.30 g, 82%).

Step 2. Compound 3l-2—

To a solution of 3l-1 (2.30 g, 7.7 mmol) in anhydrous DCM (50 mL) was added pyridinium dichromate (PDC) (5.80 g, 15.4 mmol), followed by acetic anhydride (7.87 g, 77.18 mmol) and tert-butyl alcohol (11.40 g, 154.0 mmol). The resulting solution was stirred at RT for 3 h. The mixture was loaded on a very short silica gel column and eluted with EA. The fractions containing 3l-2 were combined and concentrated. Chromatography on silica gel with EA/hexanes (1:1 to 3:2) gave 3l-2 as a white foam (2.07 g, 73%).

Step 3. Compound 3l-3—

NaBD₄ (1.10 g, 26.22 mmol) was added to a solution of 3l-2 (2.07 g, 6.9 mmol) at RT and the resulting mixture stirred at 80° C. overnight. The reaction was quenched with acetic acid (AcOH) at 0° C. The mixture was diluted with EA and washed with brine. The organic phase was dried and concentrated. The residue was purified by chromatography on silica gel (2-5% MeOH in DCM) to give 3l-3 as a white foam (854 mg, 50.83%).

Step 4. Compound 3l-4—

Compound 3l-3 (850 mg, 2.8 mmol) was dissolved in 95% trifluoroacetic acid (TFA)/5% water at 0° C. and then stirred at RT for 30 minutes. The solvent was evaporated and the residue was purified by chromatography on silica gel (5-10% MeOH in DCM) to give 3l-4 (663 mg, 90%). ¹H NMR (CD₃OD, 400 MHz) δ 8.16 (d, 1H), 5.98 (s, 1H), 5.69 (d, 1H), 3.86-3.92 (m, 2H), 1.13 (s, 3H); ESI-MS: m/z 261.1 [M+H]⁺.

Step 5. Compound 3l—

To a suspension of 3l-4 (150 mg, 0.57 mmol) in anhydrous acetonitrile (1.0 mL) was added N-methylimidazole (0.5 mL), followed by 2b (1.7 mmol, 1 M in CH₃CN) at RT. The resulting solution was stirred at RT for 24 h. The mixture was diluted with EA and concentrated. The residue was purified by RP HPLC (0.5 HCOOH in MeCN and water) to give 3l as a white solid (two isomers, 122 mg, 39%). ¹H NMR (CD₃OD, 400 MHz) δ7.79, 7.87 (2d, J=8.0 Hz, 1H), 7.20-7.38 (m, 5H), 5.98, 6.01 (2s, 1H), 5.59, 5.62 (2d, J=8.0 Hz, 1H), 4.99-5.01 (m, 1H), 4.10-4.12 (m, 2H), 3.82-3.84 (m, 1H), 1.34, 1.38 (2d, J=7.2 Hz, 3H), 1.24, 1.25 (2s, 3H), 1.17, 1.26 (2d, J=6.0 Hz, 6H); ³¹P NMR (CD₃OD, 162 MHz) δ68.42, 68.21; ESI-LCMS: m/z 546.1 [M+H]⁺.

Example 14 Preparation of 3′-O-acetyl-5′-dideuterated 2′-C-methyluridine 5′-(O-phenyl-N—(S)-1-(isopropoxycarbonyl)ethyl)thiophosphoramidate (4d)

To a suspension of 3l (750 mg, 1.38 mmol) in dry pyridine (50 mL) was added acetic anhydride (704 mg, 6.9 mmol). The reaction mixture was heated at 35° C. for 16 h. The reaction was quenched with water and the solvent was removed. The residue was purified on a silica gel column (1˜3% MeOH in DCM) to give 4d as a white solid (710 mg, 88%). ¹H NMR (CD₃OD, 400 MHz) δ7.78, 7.84 (2d, J=8.0 Hz, 1H), 7.38-7.34 (m, 2H), 7.17-7.38 (m, 5H), 5.99, 6.02 (2s, 1H), 5.59, 5.61 (2d, J=8.0 Hz, 1H), 5.13, 5.17 (2d, J=9.2 Hz, 1H), 5.04-4.97 (m, 1H), 4.52-4.25 (m, 3H), 4.14-4.06 (m, 1H), 2.16 (s, 3H), 1.35, 1.38 (2d, J=7.2 Hz, 1H), 1.18-1.24 (m, 9H); ³¹P NMR (CD₃OD, 162 MHz) δ68.90, 68.23; ESI-LCMS: m/z=585.9 [M+H]⁺.

Example 15 Preparation of 2′-C-methylthymidine 5′-(O-phenyl-N—(S)-1-(isopropoxycarbonyl)ethyl)thiophosphoramidate (3m)

Step 1. Compound 3m-2—

To a suspension of thymine (0.869 g, 5.63 mmol) in acetonitrile (27 mL) was added N, O-bis(trimethylsilyl)acetamide (5 mL) and the mixture was refluxed for 2 hours. The resulting solution was cooled to ambient temperature and a solution of 3m-1 (2.0 g, 3.45 mmol) in acetonitrile (10 mL) was added. Then SnCl₄ (1.6 mL, 13.6 mmol) was slowly added and the reaction mixture was heated to 100° C. for 5 h. The reaction mixture was cooled to 0° C. and solid NaHCO₃ was added, and a minimal amount of ice was added into the mixture. The reaction mixture was partially concentrated, diluted with EA and treated with a cold saturated aqueous solution of NaHCO₃. The salts were filtered through celite and extracted with EA. The organic phase was washed successively with a saturated aqueous solution of NaHCO₃ and brine, dried by anhydrous Na₂SO₄, and concentrated to dryness. The residue was purified by silica gel column (0-20% EA in CH₂Cl₂) to give 3m-2 (1.6 g, 85%) as a white solid.

Step 2. Compound 3m-3—

Compound 3m-2 (1.6 g, 2.74 mmol) was dissolved in methanolic ammonia (120 mL, saturated at 0° C.). The mixture was stirred at RT for 20 hours. The solution was evaporated to dryness and the residue was purified on a silica gel column (DCM:MeOH=100:1 to 50:1) to give 3m-3 as a light yellow foam (620 mg, 83.1%). ¹H NMR (MeOD, 400 MHz) δ8.05 (s, 1H), 5.93 (s, 1H), 4.01-3.97 (m, 1H), 3.91-3.86 (m, 2H), 3.80-3.76 (m, 1H), 1.85 (s, 3H), 1.13 (s, 3H).

Step 3. Compound 3m—

To a suspension of 3m-3 (150 mg, 0.55 mmol) in anhydrous CH₃CN (3 mL) was added N-methylimidazole (0.4 mL), followed by addition of 2b (530 mg, 1.65 mmol) in anhydrous CH₃CN (1 mL). The resulting solution was stirred at RT for 12 h. The reaction was quenched with water and the solvent was removed. The residue was purified by RP HPLC (0.5 HCOOH in MeCN and water) to give compound 3m as a white solid (two isomers, 43 mg, 14.0%). ¹H NMR (MeOD, 400 MHz) δ7.54, 7.64 (2s, 1H), 7.16˜7.36 (m, 5H), 5.98, 6.01 (2s, 1H). 5.02˜4.94 (m, 1H), 4.56˜4.52 (m, 1H), 4.43˜4.29 (m, 1H), 4.17˜4.02 (m, 2H), 3.94˜3.84 (m, 1H), 1.81, 1.84 (2s, 3H), 1.31, 1.36 (2d, J=7.2 Hz, 3H), 1.25˜1.23 (m, 6H), 1.15 (s, 3H); ³¹P NMR (MeOD, 162 MHz) δ69.17, 68.68; ESI-LCMS: m/z=558.1 [M+H]⁺.

Example 16 Preparation of 1-(2-amino-6-cyclopropylaminopurin-9-yl)-2-C-methyl-β-D-ribofuranose 5-(O-phenyl-N—(S)-1-(isopropoxycarbonyl)ethyl)thiophosphoramidate (3z)

Step 1. Compound 3z-1—

To a solution of compound 3m-1 (20.0 g, 34.47 mmol) and 6-chloro-2-aminopurine (5.90 g, 34.91 mmol) in anhydrous MeCN (300 mL) was added 1,8-diazabicycloundec-7-ene (DBU) (15.8 g, 103.9 mmol) at 0° C. The mixture was stirred at 0° C. for 5 minutes and then trimethylsilyltrifluoromethane sulfonate (TMSOTf) (27.0 mL, 137.8 mmol) was added dropwise. Stirring was continued for another 30 minutes and then the mixture was heated to 70° C. and stirred for 18 hour. The reaction was then cooled to RT and diluted with EA. The solution was washed with saturated NaHCO₃ and brine. The organic layer was dried over Na₂SO₄ and then concentrated. The residue was purified by a silica gel column (20˜40% EA in PE) and then RP HPLC (0.5% HCOOH in MeCN and water) to give compound 23-2 as a white solid (5.4 g, 25.6%). ¹H NMR (DMSO-d6, 400 MHz) δ8.38 (s, 1H), 7.97-8.05 (m, 4H), 7.82-7.85 (m, 2H), 7.58-7.66 (m, 3H), 7.39-7.53 (m, 4H), 7.18-7.37 (m, 2H), 7.19 (brs, 2H), 6.61 (s, 1H), 5.94 (d, J=4.8 Hz, 1H), 4.70-4.89 (m, 3H), 1.58 (s, 3H).

Step 2. Preparation of compound 3z-2—

Compound 3z-1 (100 mg, 0.16 mmol) and THF (10 mL) were placed into a dry flask and then cyclopropyl amine (1.61 g, 28.21 mmol) was added. After the addition, the mixture was heated to reflux overnight. Then the solvent was removed and the residue was purified on a silica gel column (2˜10% MeOH in DCM) to give 3z-2 as a white solid (82 mg, 77.6%).

Step 3. Compound 3z-3—

Compound 3z-2 (402 mg, 0.62 mmol) was dissolved in methanolic ammonia (20 mL, saturated at 0° C.) and the mixture was stirred at RT for 12 hours. The solvent was removed and the residue was purified on a silica gel column (2˜10% MeOH in DCM) to give 3z-3 as a white solid (149 mg, 72.4%). ¹H NMR (CD₃OD, 400 MHz) δ8.14 (d, J=11.2 Hz, 1H), 5.93 (s, 1H), 4.22 (d, J=8.4 Hz, 1H), 4.03 (d, J=10.8 Hz, 2H), 3.86 (d, J₁=12.8 Hz, J₂=3.2 Hz, 1H), 2.91 (s, 1H), 0.79-0.98 (m, 2H), 0.61-0.70 (m, 2H); ESI-LCMS: m/z 337.1 [M+H]⁺, 360.1 [M+Na]⁺.

Step 4. Compound 3z—

To a stirred suspension of 3z-3 (110 mg, 0.33 mmol) in anhydrous acetonitrile (1.0 mL) was added N-methylimidazole (0.5 mL) followed by slow addition of 2b (1.05 g, 3.273 mmol, 1M in MeCN) at RT. The resulting solution was stirred at 50° C. for 4 hours and then diluted with EA. The solution was washed with 10% AcOH/H₂O, brine, 5% NaHCO₃ aqueous solution, and dried over Na₂SO₄. The solvent was removed and the residue was purified by RP HPLC (0.5% HCOOH in MeCN and water) to give 3z as a white solid (two isomers, 131 mg, 64%). ¹H NMR (CD₃OD, 400 MHz) δ7.96, 8.00 (2s, 1H), 7.28-7.36 (m, 5H), 7.14-7.20 (m, 1H), 5.96, 5.99 (2s, 1H), 4.92-4.98 (m, 1H), 4.37-4.57 (m, 2H), 4.04-4.23 (m, 3H), 2.91 (br, 1H), 1.36, 1.32 (2d, J=7.2 Hz, 3H), 1.17-1.23 (m, 7H), 0.96, 0.99 (2s, 3H), 0.87-0.90 (m, 2H), 0.63-0.69 (m, 2H); ³¹P NMR (CD₃OD, 162 MHz) δ 68.53, 68.38; ESI-LCMS: m/z 622.2 [M+H]⁺, 644.2 [M+Na]⁺.

Example 17 Preparation of 1-(2,6-diaminopurin-9-yl)-2-C-methyl-β-D-ribofuranose 5-(O-phenyl-N—(S)-1-(isopropoxycarbonyl)ethyl)thiophosphoramidate (3aa)

Step 1. Compound 3aa-1—

Compound 3z-1 (1.01 g, 1.56 mmol) was suspended in aqueous ammonia (28%, 40 mL) and dioxane (4 mL) in a sealed vessel. The mixture was heated at 100° C. overnight. Then the solvent was removed and the residue was purification on a silica gel column (2˜10% MeOH in DCM) to give 3aa-1 as a white solid (418 mg, 88.9%). ¹H NMR (CD₃OD, 400 MHz) δ88.17 (s, 1H), 5.93 (s, 1H), 4.24 (d, J=8.8 Hz, 1H), 4.01-4.04 (m, 2H), 3.86 (dd, J₁=12.8 Hz, J₂=3.2 Hz, 1H), 0.96 (s, 3H); ESI-LCMS: m/z 297.1 [M+H]⁺.

Step 2. Compound 3aa—

To a stirred suspension of 3aa-1 (62 mg, 0.20 mmol) in anhydrous acetonitrile (1.0 mL) was added N-methylimidazole (0.5 mL) followed by slow addition of 2b (652 mg, 2.02 mmol, 1M in MeCN) at RT. The resulting solution was stirred at RT for 24 hours. The solution was diluted with EA and washed with 10% AcOH in H₂O, brine, 5% NaHCO₃ aqueous solution, and dried over Na₂SO₄. The solvent was removed and the residue was purified by RP HPLC (0.5% HCOOH in MeCN and water) to give 3aa as a white solid (31 mg, 25.6%). ¹H NMR (DMSO-d6, 400 MHz) δ77.81, 7.83 (2s, 1H), 7.33-7.38 (m, 2H), 7.17-7.25 (m, 3H), 6.58-6.78 (m, 3H), 5.81-5.83 (m, 3H), 5.32-5.43 (m, 1H), 5.19, 5.20 (2s, 1H), 4.78-4.85 (m, 1H), 4.21-4.42 (m, 2H), 3.87-4.15 (m, 3H), 1.24-1.26 (m, 3H), 1.08-1.15 (m, 6H), 0.83, 0.84 (2s, 3H); ³¹P NMR (DMSO-d6, 162 MHz) δ 68.19, 67.90; ESI-LCMS: m/z 589.1[M+H]⁺, 604.1 [M+Na]⁺.

Example 18 Preparation of 1-(2-amino-6-allylaminopurin-9-yl)-2-C-methyl-β-D-ribofuranose 5-(O-phenyl-N—(S)-1-(isopropoxycarbonyl)ethyl)thiophosphoramidate (3bb)

Step 1. Compound 3bb-1—

A mixture of 3z-1 (802 mg, 1.27 mmol) and ally amine (7.26 g, 127.3 mmol) in THF (30 mL) was refluxed overnight. The solvent was removed and the residue was purified on a silica gel column (2˜10% MeOH in DCM) to give crude 3bb-1 (405 mg), which was dissolved in 20 mL methanolic ammonia (saturated at 0° C.). The mixture was stirred at RT for 12 hours. The solvent was removed and the residue was purified on a silica gel column (2˜10% MeOH in DCM) to give 3bb-1 as a white solid (153 mg, 35.9%). ¹H NMR (CD₃OD, 400 MHz) δ8.10 (s, 1H), 5.92-6.03 (m, 2H), 5.27 (d, J=17.6 Hz, 1H), 5.14 (d, J=10.4 Hz, 1H), 4.18-4.24 (m, 3H), 4.03 (d, J=10.0 Hz, 2H), 3.86 (d, J=10.4 Hz, 1H), 0.95 (s, 3H); ESI-LCMS: m/z 337.1 [M+H]⁺.

Step 2. Compound 3bb—

To a stirred suspension of 3bb-1 (200 mg, 0.59 mmol) in anhydrous acetonitrile (1.0 mL) was added N-methylimidazole (0.5 mL) followed by 2b (573 mg, 1.79 mmol, 1M in MeCN) at RT. The resulting solution was stirred at RT for 24 hrs and then was diluted with EA. The solution was washed with 10% AcOH in H₂O, brine and 5% NaHCO₃ aqueous solution. The organic solution was dried and concentrated. The residue was purified by RP HPLC (0.5% HCOOH in MeCN and water) to give 3bb as a white solid (two isomers, 155 mg, 40.8%). ¹H NMR (CD₃OD, 400 MHz) δ 7.94, 7.98 (2s, 1H), 7.29-7.34 (m, 4H), 7.18-7.28 (m, 1H), 5.96-6.09 (m, 2H), 5.27, 5.31 (2s, 1H), 5.15, 5.17 (2d, J=1.2 Hz, 1H), 4.92-4.96 (m, 1H), 4.35-4.57 (m, 2H), 4.01-4.28 (m, 5H), 1.32, 1.36 (2d, J=7.2 Hz, 3H), 1.16-1.25 (m, 6H), 0.97 (2s, 3H); ³¹P NMR (CD₃OD, 160 MHz) δ 68.51, 68.40; ESI-LCMS: m/z 622.1 [M+H]⁺, 644.1 [M+Na]⁺.

Example 19 Preparation of 1-(2-amino-6-chloropurin-9-yl)-2-C-methyl-β-D-ribofuranose 5-(O-phenyl-N—(S)-1-(isopropoxycarbonyl)ethyl)thiophosphoramidate (3cc)

Step 1. Compound 3cc-1—

Compound 3z-1 (506 mg, 0.79 mmol) was dissolved in 100 mL of methanolic ammonia and the mixture was stirred at RT for 12 h. The solvent was removed and the residue was purified on a silica gel column (2˜10% MeOH in DCM) to give 3cc-1 as a white solid (204 mg, yield: 79.9%).

Step 2. Compound 3cc—

To a stirred suspension of 3cc-1 (198 mg, 0.63 mmol) in anhydrous acetonitrile (1.0 mL) was added N-methylimidazole (0.5 mL) followed by 2b (611 mg, 1.904 mmol, 1M in MeCN) at RT. The resulting solution was stirred at 30-40° C. for 12 hours and then diluted with EA. The solution was washed with 10% AcOH in H₂O, brine, and 5% NaHCO₃. The organic phase was dried and concentrated. The residue was purified by RP HPLC (0.5% HCOOH in MeCN and water) to give 3cc as a white solid (118 mg, 31.6%). ¹H NMR (CD₃OD, 400 MHz) δ 8.25, 8.28 (2s, 1H), 7.27-7.35 (m, 4H), 7.15-7.18 (m, 1H), 6.02, 6.05 (2s, 1H), 4.93-4.98 (m, 1H), 4.40-4.54 (m, 2H), 4.20-4.27 (m, 2H), 4.05-4.13 (m, 1H), 1.15-1.35 (m, 9H), 0.99, 1.01 (2s, 3H); ³¹P NMR (CD₃OD, 162 MHz) δ68.66, 68.53; ESI-LCMS: m/z 601.1 [M+H]⁺.

Example 20 Preparation of 2′-C-methyluridine 5′-(O-phenyl-N—(S)-1-(isopropoxycarbonyl)isobutyl)thiophosphoramidate (3n)

To a solution of 2′-C-methyluridine (150 mg, 0.581 mmol) in MeCN (1 mL) and N-methylimidazole (0.7 mL) was added 2h (651 mg, 1.86 mmol). The mixture was stirred at RT for 3 days. The solvent was removed and the residue was purified by RP HPLC (0.1% HCOOH in MeCN and water) to give 3n as a white solid (two isomers, 22 mg, 6.6%). ¹H NMR (CD₃OD, 400 MHz) δ7.76, 7.78 (2d, J=9.2 Hz, 1H), 7.14-7.35 (m, 5H), 5.95, 5.97 (2s, 1H), 5.56, 5.63 (2d, J=8.4 Hz, 1H), 4.95-5.03 (m, 1H), 4.44-4.56 (m, 1H), 4.30-4.41 (M, 1H), 4.08-4.11 (m, 1H), 3.75-3.90 (m, 2H), 2.00-2.07 (m, 1H), 1.12-1.25 (m, 6H), 1.11, 1.15 (2s, 3H), 0.87-0.97 (m, 6H); ³¹P NMR (CD₃OD, 162 MHz) δ70.38, 69.13; ESI-LCMS: m/z 572 [M+H]⁺.

Example 21 Preparation of 2′-C-methyluridine 5′-(O-phenyl-N—(S)-1-(isopropoxycarbonyl)isopentyl)thiophosphoramidate (3o)

Compound 3o was prepared using the procedure for preparing compound 3n, with 2i in place of 2h. ¹H NMR (CD₃OD, 400 M Hz) δ 7.77, 7.84 (2d, J=8.0 Hz, 1H), 7.14-7.35 (m, 5H), 5.96 (2s, 1H), 5.57, 5.62 (2d, J=8.0 Hz, 1H), 4.84-4.98 (m, 1H), 4.46-4.53 (m, 1H), 4.28-4.42 (m, 1H), 3.97-4.12 (m, 2H), 3.80 (2s, 1H), 1.58-1.81 (m, 1H), 1.48-1.56 (m, 2H), 1.20-1.23 (m, 6H), 1.13 (2s, 3H), 0.81-0.92 (m, 6H); ³¹P NMR (CD₃OD, 400 MHz) δ 68.56, 69.15; ESI-MS: m/z 586 [M+H]⁺, m/z 608 [M+Na]⁺.

Example 22 Preparation of 2′-C-methylguanosine 5′-(O-phenyl-N—(S)-1-(cyclohexoxycarbonyl)ethyl)thiophosphoramidate (3s)

To a stirred suspension of commercial 2′-C-methylguanosine (100 mg, 0.34 mmol) in anhydrous acetonitrile (1.5 mL) was added N-methylimidazole (0.56 mL, 6.8 mmol, 20 equivalent) followed by 2c (303 mg, 0.84 mmol, 1M in MeCN) at RT. The resulting solution was stirred at 40° C. for 3 hours and then diluted with EA. The solution was washed with 10% AcOH in H₂O, and brine. The organic layer was separated, dried over anhydrous Na₂SO₄ and filtered. The filtrate was concentrated in vacuum to give a residue which was purified on a silica gel column (3˜7% MeOH in DCM). The collected fractions were concentrated and re-purified on a silica gel column (2˜5% MeOH in DCM) to give (127.8 mg, 61.2%) of 3s as a white solid. ¹H NMR (DMSO-d₆, 400 MHz) δ 10.6 (s, 1H), 7.76 (d, J=5.6 Hz, 1H), 7.36-7.31 (m, 2H), 7.22-7.01 (m, 4H), 6.56-6.48 (m, 3H), 5.74 (d, J=8.4 Hz, 1H), 5.42 & 5.35 (2d, each J=6.4 Hz, 1H), 5.16 (d, J=2.8 Hz, 1H), 4.62-3.93 (m, 6H), 1.67-1.58 (m, 5H), 1.33-1.16 (m, 12H), 0.79 (s, 3H); ³¹P NMR (DMSO-d₆) δ 68.07, 67.71; ESI-LCMS: m/z=623.1 [M+H]⁺.

Example 23 Preparation of 2′-C-Methylguanosine 5′-(O-phenyl-N—(S)-1-(isopropoxycarbonyl)ethyl)thiophosphoramidate (3r)

Compound 3r was prepared using the procedure for preparing compound 3s, with 2b in place of 2c. ¹H NMR (DMSO-d₆, 400 MHz) δ10.6 (s, 1H), 7.76 (d, J=1.6 Hz, 1H), 7.34-7.31 (m, 2H), 7.22-7.14 (m, 4H), 6.62-6.48 (m, 3H), 5.74 (d, J=7.2 Hz, 1H), 5.42 & 5.33 (2d, each J=6.8 Hz, 1H), 5.16 (d, J=2.4 Hz, 1H), 4.84-3.77 (m, 1H), 4.42-3.85 (m, 5H), 1.25-1.1 (m, 12H), 0.81 & 0.8 (2s, 3H); ³¹P NMR (DMSO-d₆) δ 68.23, 67.64; ESI-LCMS: m/z=583.4 [M+H]⁺.

Example 24 Preparation of 2′-Deoxy-2′-fluoro-2′-C-methyl-6-methoxyguanosine 5′-(O-phenyl-N—(S)-1-(isopropoxycarbonyl)ethyl)-thiophosphoramidate (3t)

Compound 3t was prepared using the procedure for preparing compound 3s, with 2b in place of 2c, and with 2′-deoxy-2′-fluoro-2′-C-methyl-6-methoxyguanosine in place of 2′-C-methylguanosine. ¹H NMR (DMSO-d₆, 400 MHz) δ 7.96 & 9.95 (2s, 1H), 7.36-7.29 (m, 2H), 7.21-7.14 (m, 3H), 6.57 (br s, 2H), 6.1 & 6.05 (2d, each J=8.8 Hz, 1H), 5.75 (br s, 2H), 4.82-4.76 (m, 1H), 4.45-4.04 (m, 3H), 3.93 (s, 3H), 1.24-1.13 (m, 3H), 1.12-1.03 (m, 9H); ³¹P NMR (DMSO-d₆) δ68.21, 67.82; ESI-LCMS: m/z=599.4 [M+H]⁺.

Example 25 Preparation of 1-(2-Amino-6-methoxypurin-9-yl)-2-C-methyl-β-D-ribofuranose 5-(O-phenyl-N—(S)-1-(isopropoxycarbonyl)ethyl)-thiophosphoramidate (3u)

Compound 3u was prepared using the procedure for preparing compound 3s, with 2b in place of 2c, and with 1-(2-Amino-6-methoxypurin-9-yl)-2-C-methyl-β-D-ribofuranose in place of 2′-C-methylguanosine. ¹H NMR (DMSO-d₆, 400 MHz) δ7.93 (s, 1H), 7.35-7.30 (m, 2H), 7.22-7.14 (m, 3H), 6.61-6.52 (m, 1H), 6.48 (br s, 2H), 5.86 (d, each J=5.2 Hz, 1H), 5.43, 5.32 (br s, 1H), 5.20 (br s, 1H), 4.84-4.76 (m, 1H), 4.36-4.04 (m, 4H), 3.93 (s, 3H), 1.24-1.15 (m, 3H), 1.19-1.06 (m, 6H), 0.8-0.78 (m, 3H); ³¹P NMR (DMSO-d₆) δ 68.21, 67.65; ESI-LCMS: m/z=597.5 [M+H]⁺.

Example 26 Preparation of 2′-Deoxy-2′-α-fluoro-2′-β-C-methylguanosine 5′-(O-phenyl-N—(S)-1-(neopentoxycarbonylethyl)thiophosphoramidate (3q)

Compound 3q was prepared using the procedure for preparing compound 3s, with 2d in place of 2c, and with 2′-deoxy-2′-α-fluoro-2′-β-C-methylguanosine in place of 2′-C-methylguanosine. ¹H NMR (DMSO-d₆, 400 MHz) δ 10.66 (br s, 1H), 7.79 (s, 1H), 7.36-7.30 (m, 2H), 7.22-7.15 (m, 3H), 6.61-6.52 (m, 1H), 6.48 (br s, 2H), 6.72-6.56 (m, 3H), 6.00, 5.95 (2d, J=8.0, 8.4 Hz, 1H), 5.75-5.82 (m, 1H), 4.43-3.92 (m, 5H), 3.76-3.53 (m, 2H), 1.29-1.24 (m, 3H), 1.09-1.00 (m, 4H), 0.84, 0.81 (2s, 8H); ³¹P NMR (DMSO-d₆) δ 68.09, 68.03; ESI-LCMS: m/z=613.7 [M+H]⁺.

Example 27 Preparation of 2′-C-Methyladenosine 5′-(O-phenyl-N—(S)-1-(neopentoxycarbonyl)ethyl)thiophosphoramidate (3dd)

Compound 3dd was prepared using the procedure for preparing compound 3s, with 2d in place of 2c, and with 2′-C-methyladenosine in place of 2′-C-methylguanosine. ¹H NMR (DMSO-d₆, 400 MHz) δ 8.22, 8.2 (2s, 1H), 8.12 (s, 1H), 7.36-7.13 (m, 6H), 6.61-6.55 (m, 1H), 5.97, 5.94 (2s, 1H), 5.40, 5.34, 5.31 (3d, J=6.8, 6.8, 6.0 Hz, 2H), 4.39-3.99 (m, 5H), 3.76-3.61 (m, 2H), 3.42 (d, J=10.4 Hz, 1H), 1.27-1.23 (m, 3H), 0.83, 0.77 (2s, 4H), 0.77, 0.76 (2s, 8H); ³¹P NMR (DMSO-d₆) δ68.15, 67.74; ESI-LCMS: m/z=595.0 [M+H]⁺.

Example 28 Preparation of 2′-C-Methyladenosine 5′-(O-(1-naphthyl)-N—(S)-1-(isopropoxycarbonyl)ethyl)thiophosphoramidate (3ee)

Compound 3dd was prepared using the procedure for preparing compound 3s, with 2e in place of 2c, and with 2′-C-methyladenosine in place of 2′-C-methylguanosine. ¹H NMR (DMSO-d₆, 400 MHz) δ 8.28, 8.24 (2s, 1H), 8.12-8.06 (m, 2H), 7.93-7.91 (m, 1H), 7.29-7.68 (m, 1H), 7.54-7.37 (m, 4H), 7.26 (br s, 2H), 6.82-6.72 (m, 1H), 6.00, 5.98 (2s, 1H), 5.47, 5.39, 5.31 (3d, J=6.4, 6.8, 10.0 Hz, 2H), 4.82-4.74 (m, 1H), 4.48-4.35 (m, 2H), 4.28-4.15 (m, 2H), 4.03-3.96 (m, 1H), 1.27-1.24 (m, 3H), 1.1-1.00 (m, 6H), 0.8 (s, 3H); ESI-LCMS: m/z=617.1 [M+H]⁺.

Example 29 Preparation of 2′-C-methylguanosine 5′-(O-phenyl-N—(S)-1-(neopentoxycarbonyl)ethyl)thiophosphoramidate (3p)

Step 1. Compound 3p-1—

A mixture of 2′-C-methylguanosine (1.0 g, 3.36 mmol), trimethyl orthoformate (20 mL) and p-toluenesulfonic acid monohydrate (961 mg, 5.05 mmol) in 1,4-dioxane (30 mL) was stirred at RT for 24 h. Dowex MWA-1 basic resin we added and stirred until the solution was neutralized. The resin was filtered and washed thoroughly with MeOH and then with MeOH/DCM (1:1). The filtrate was concentrated and the residue was subjected to flash chromatography on a silica gel column eluting with 5-10% MeOH in DCM to give (0.94 g) of 3p-1 as a white solid.

Step 2. Compound 3p-2—

A solution of 3p-1 (0.94 g, 2.77 mmol), dimethylaminopyridine (DMAP) (338 mg, 2.77 mmol) and t-butyldimethylsilyl chloride (TBSCl) (543 mg, 3.60 mmol) in pyridine (10 mL) was stirred at 25° C. overnight. 4-Methoxytrityl chloride (1.56 g, 5.0 mmol) was added and the resulting mixture stirred at RT 50° C. for 3 h. The mixture was diluted with ethyl acetate, and washed with brine three times. The solvent was evaporated and the residue was chromatographed on silica gel with 3-5% MeOH in DCM to give 1.66 g of a protected intermediate as foam solid. A solution of the intermediate (1.66 g, 2.66 mmol) and 1.0 M tetrabutylammonium fluoride (TBAF)/THF (4 mL) in 10 mL of THF stood at RT for 20 h. The solution was concentrated. The residue was subjected to flash chromatography on silica gel with 5-6% MeOH in DCM to give 1.33 g of 3p-2 as a white foam. MS m/z 611.9 (MH⁺).

Step 3. Compound 3p—

Compound 2d (1.0 M in MeCN, 0.5 mL) was added dropwise to a solution of 3p-2 (61 mg, 0.1 mmol) and diisopropylethylamine (0.3 mL) in anhydrous acetonitrile (0.4 mL). The resulting solution was heated at 82° C. for 20 h, diluted with ethyl acetate, washed with brine three times, dried over sodium sulfate, and concentrated. Chromatography on silica gel with 20-30% ethyl acetate in hexanes gave 82 mg of a protected intermediate as a white foam, which was dissolved in a mixture of 80% formic acid and 20% water (3 mL). The solution stood at RT overnight, was concentrated, and then co-evaporated with MeOH/toluene three times. Chromatography on silica gel with 6-10% MeOH in DCM gave 27 mg of 3p as a white solid; ¹H NMR (acetone-d₆) δ 7.83, 7.92 (2s, 1H), 7.10-7.34 (m, 5H), 5.88, 5.90 (2s, 1H), 4.33-3.53 (m, 2H), 4.11-4.24 (m, 3H), 3.61-3.79 (m, 2H), 1.39, 1.36 (2d, J=7.2 Hz, 3H), 0.94, 0.95 (2s, 3H), 0.84, 0.87 (2s, 9H); ³¹P NMR (acetone-d₆) δ68.27, 67.85; ESI-LCMS: m/z 611.3 [M+H]⁺.

Example 30 Preparation of 2′,5′(S)—C,C-Dimethyladenosine 5′-(O-phenyl-N—(S)-1-(neopentoxycarbonyl)ethyl)thiophosphoramidate (3hh)

Compound 3hh was prepared using the procedure for preparing compound 3p, with 2′,5′-C,C-dimethyladenosine in place of 2′-C-methylguanosine. ¹H NMR (CD₃OD) δ 8.40, 8.36 (2s, 1H), 8.22, 8.20 (2s, 1H), 7.07-7.36 (m, 5H), 6.06, 6.05 (2d, J=5.2 Hz, 1H), 5.88, 5.90 (2s, 1H), 4.59 (t, J=5.2 Hz, 0.5H), 4.50 (q, J=5.2 Hz, 1H), 4.40 (q, J=3.6, 5.2 Hz, 0.5H), 4.04-4.19 (m, 2H), 3.81 (d, J=0.8 Hz, 1H), 3.75 (d, J=10.4 Hz, 1H), 3.65 (d, J=10.4 Hz, 1H), 1.52, 1.40 (2d, J=6.4 Hz, 3H), 1.29, 1.30 (2s, 3H), 0.93, 0.87 (2s, 9H); ³¹P NMR (acetone-d₆) δ68.40, 67.43; ESI-LCMS: m/z 595.1 [M+H]⁺.

Example 31 Preparation of 1-(2-Amino-6-methoxypurin-9-yl)-2-C-methyl-β-D-ribofuranose 5-(O-phenyl-N—(S)-1-(neopentoxycarbonyl)ethyl)-thiophosphoramidate (3v)

Compound 3v was prepared using the procedure for preparing compound 3p, with 1-(2-amino-6-methoxypurin-9-yl)-2-C-methyl-β-D-ribofuranose in place of 2′-C-methylguanosine. ¹H NMR (CD₃OD, 400 MHz) δ 7.97, 8.00 (2s, 1H), 7.10-7.33 (m, 5H), 5.99, 5.96 (2s, 1H), 4.33-4.55 (m, 2H), 4.031, 4.034 (2s, 3H), 3.56-3.72 (m, 2H), 1.31-1.36 (m, 3H), 0.94, 0.92 (2s, 3H), 0.89, 0.85 (2s, 9H); ³¹P NMR (DMSO-d₆) δ68.52, 68.27. ESI-LCMS: m/z 625.3 [M+H]⁺.

Example 32 Preparation of 1-(2-Amino-6-methoxypurin-9-yl)-2-C-methyl-β-D-ribofuranose 5-(O-phenyl-N—(S)-1-(cyclohexoxycarbonyl)ethyl)-thiophosphoramidate (3w)

Compound 3w was prepared using the procedure for preparing compound 3p, with 2c in place of 2d, and with 1-(2-Amino-6-methoxypurin-9-yl)-2-C-methyl-β-D-ribofuranose in place of 2′-C-methylguanosine. ¹H NMR (CD₃OD, 400 MHz) δ87.98, 8.01 (2s, 1H), 7.24-7.32 (m, 4H), 7.10-7.17 (m, 1H), 6.00, 5.96 (2s, 1H), 4.36-4.73 (m, 3H), 4.036, 4.034 (2s, 3H), 4.01-4.22 (m, 3H), 1.60-1.80 (m, 4H), 1.19-1.55 (m, 9H), 0.92, 0.94 (2s, 3H); ³¹P NMR (DMSO-d₆) δ68.43, 68.32. ESI-LCMS: m/z 637.6 [M+H]⁺.

Example 33 Preparation of 1-(2-Amino-6-methoxypurin-9-yl)-2-C-methyl-β-D-ribofuranose 5-(O-(1-naphthyl)-N—(S)-1-(neopentoxycarbonyl)ethyl)-thiophosphoramidate (3x)

Compound 3x was prepared using the procedure for preparing compound 3p, with 2g in place of 2d, and with 1-(2-Amino-6-methoxypurin-9-yl)-2-C-methyl-β-D-ribofuranose in place of 2′-C-methylguanosine. ¹H NMR (CD₃OD, 400 MHz) δ 8.15-8.19 (m, 1H), 8.03, 7.97 (2s, 1H), 7.80-7.85 (m, 1H), 7.31-7.67 (m, 5H), 6.00, 5.98 (2s, 1H), 4.43-4.62 (m, 2H), 4.18-4.27 (m, 3H), 4.01 (s, 3H), 3.57-3.79 (m, 2H), 1.33-1.37 (m, 3H), 0.941, 0.946 (2s, 3H), 0.855, 0.848 (2s, 9H); ³¹P NMR (DMSO-d₆) δ68.55, 68.57. ESI-LCMS: m/z 675.3 [M+H]⁺.

Example 34 Preparation of additional 2′-C-methyluridine 5′-thiophosphoramidates

Compounds 3ii-3vv, as shown in Table 8, were prepared using a similar procedure for preparing compound 3n.

TABLE 8 ³¹P NMR Compound ppm

69.30 69.09

68.92 68.58

68.45 68.16

69.69 69.28

68.60 68.42

68.25 67.79

69.25 69.12

69.52 68.53

70.03 69.56

68.87 68.76

70.83 69.38

69.12 68.45

69.14 68.46

68.74 66.82

Example 35 Preparation of 2′-C-Methyl-3′-O-propionyluridine 5′-(O-phenyl-N—(S)-1-(isopropoxycarbonyl)ethyl)-thiophosphoramidate (4b)

Compound 3b (1 g, 1.88 mmol) was dissolved in 10 mL of dry pyridine, propionic anhydride was added (385 mg, 2.81 mmol) and reaction mixture was left overnight at RT. TLC showed that reaction was not completed. More anhydride (385 mg, 2.81 mmol) was added and the mixture was heated at 40° C. for 2 hours. Solvents were evaporated. The residue was distributed between ethyl acetate and water. The organic layer was washed with water, brine, dried over Na₂SO₄, and concentrated. Purification by column chromatography on silica gel in a gradient of methanol in DCM from 2% to 7% resulted in 725 mg of 4b (64%). ¹H NMR (CDCl₃): δ 8.70 & 8.66 (2s, 1H), 7.59-7.48 (2d, 1H), 7.30-7.08 (m, 5H), 5.93 & 5.90 (2s, 1H), 5.60 & 5.49 (2d, 1H), 5.01-4.94 (m, 2H), 4.50-4.38 (m, 1H), 4.32-4.02 (m, 3H), 2.45-2.35 (m, 2H), 1.38-1.30 (m, 3H), 1.20-1.11 (m, 12H); ³¹P NMR: δ 67.72, 67.54 (1:1 mixture of diastereomers); ESI-LCMS: m/z 598.3 [M+H]⁺.

Example 36 Preparation of 2′,3′-O-diisobutyryl-2′-C-methyluridine 5′-(O-phenyl-N—(S)-1-(isopropoxycarbonyl)ethyl)thiophosphoramidate (4c) and Preparation of 2′-C-methyl-3′-O-isobutyryluridine 5′-(O-phenyl-N—(S)-1-(isopropoxycarbonyl)ethyl)thiophosphoramidate (4f)

Step 1. Compound 4c—

To a solution of 3b (0.1 g, 0.18 mmol) in anhydrous pyridine (2 mL), was added DMAP (22 mg, 0.18 mmol) followed by isobutyric anhydride (0.1 mL, 0.63 mmol) under N₂ atmosphere. The reaction mixture was stirred at RT for 1 h. The reaction was quenched by adding isopropanol (0.5 mL). The solvent was removed under vacuum and the residue was taken up into EA (100 mL). The solution was washed with saturated NaHCO₃ and brine. The organic layer was separated, dried over anhydrous Na₂SO₄ and filtered. The filtrate was concentrated in vacuum to give a residue which was purified on a silica gel column (1˜5% MeOH in DCM) to give the faster eluting product 4c as a white solid (36.5 mg). ¹H NMR (DMSO-d₆, 400 MHz) δ11.46 (s, 1H), 7.59& 7.55 (2d, J=8.4, 8.4 Hz, 1H), 7.37-7.32 (m, 2H), 7.21-7.15 (m, 3H), 6.67-6.66 (m, 1H), 6.14 & 6.11 (each s, 1H), 5.58 (d, J=8.0 Hz, 1H), 5.2 (br s, 1H), 4.88-4.84 (m, 1H), 4.28-4.27 (m, 1H), 3.95-3.85 (m, 1H), 2.54-2.49 (m, 2H), 1.38 & 1.36 (2s, 3H), 1.26-1.21 (m, 2H), 1.56-1.12 (m, 6H), 1.09-1.05 (m, 12H); ³¹P NMR (DMSO-d₆) δ68.44, 68.42; ESI-LCMS: m/z=682.4 [M−H]⁻.

Step 2. Compound 4f—

Further elution of the residue on the silica gel column using 5% MeOH in DCM gave the slower eluting product 4f (54.5 mg) as white foam after evaporation of solvent in-vacuo. ¹H NMR (DMSO-d₆, 400 MHz) δ11.42 (s, 1H), 7.65 & 7.63 (2d, J=8.0, 8.4 Hz, 1H), 7.37-7.32 (m, 2H), 7.21-7.15 (m, 3H), 6.68-6.61 (m, 1H), 5.84 & 5.81 (each s, 1H), 5.71 & 5.68 (each s, 1H), 5.56 & 5.47 (each d, each J=8.0 Hz, 1H), 4.98-4.94 (m, 1H), 4.87-4.82 (m, 1H), 4.31-4.16 (m, 3H), 3.85-3.95 (m, 1H), 2.62-2.58 (m, 1H), 1.26 & 1.2 (each d, J=7.2, 6.8 Hz, 3H), 1.16-1.08 (m, 12H), 1.01 (s, 3H); ³¹P NMR (DMSO-d₆) δ68.93, 67.96; ESI-LCMS: m/z=612.4 [M+H]⁺.

Example 37 Preparation of 2′-C-2′-O-dimethyluridine 5′-(O-phenyl-N—(S)-1-(isopropoxycarbonyl)ethyl)thiophosphoramidate (4e)

Step 1. Compound 4e-1—

To an ice-cold solution of 2′-C-methyluridine (2.0 g, 7.6 mmol) in anhydrous pyridine (20 mL) was added 1,3-dichloro-1,1,3,3-tetraisopropyldisiloxane (TIPDSCl₂) (2.40 g, 7.6 mmol) in small portions under N₂. The reaction mixture was stirred at RT overnight. The solvent was removed under vacuum and the residue was taken up into EA (100 mL). The solution was washed with saturated NaHCO₃ and brine. The organic layer was separated, dried over anhydrous Na₂SO₄ and filtered. The filtrate was concentrated in vacuum to give a residue, which was purified on a silica gel column (DCM/MeOH=100/1 to 50/1) to give 4e-1 (3.2 g, 85%) as a white foam.

Step 2. Compound 4e-2—

To a solution of 4e-1 (2.0 g, 4.0 mmol) in anhydrous THF (30 mL) was added NaH (384 mg, 16 mmol) at 0° C. The mixture was stirred at 0° C. for 30 minutes before CH₃I (1.2 g, 8 mmol) was added. Stirring was continued for 4 h at 0° C. The mixture was diluted with EA (100 mL), washed with saturated NaHCO₃ and brine. The organic layer was dried with Na₂SO₄ and concentrated to a residue which was purified on a silica gel column (DCM/MeOH=100/1 to 50/1) to give 4e-2 (556 mg, 26.93%) as a white foam.

Step 3. Compound 4e-3—

To a stirred solution of 4e-2 (556 mg, 1.08 mmol) in MeOH (10 mL) was added NH₄F (232 mg, 6.46 mmol). The mixture was stirred at 80° C. for 12 h. The solvent was removed and the residue was purified on a silica gel column (DCM/MeOH=100/1 to 20/1) to give 4e-3 (220 mg, 74%) as a white solid. ¹H NMR (DMSO-d6, 400 MHz) δ11.39 (brs, 1H), 8.07 (d, J=8.0 Hz, 1H), 5.91 (s, 1H), 5.63 (d, J=8.0 Hz, 1H), 5.21 (t, J=4.8 Hz, 1H), 5.05 (d, J=8.0 Hz, 1H), 3.78-3.82 (m, 2H), 3.59-3.71 (m, 2H), 3.36 (3, 3H), 1.08 (s, 3H); ESI-LCMS: m/z=273.1 [M+H]⁺.

Step 4. Compound 4e—

To a stirred suspension of 4e-3 (170 mg, 0.63 mmol) in anhydrous THF (2 mL) were added N-methylimidazole (0.5 mL) followed by 2b (598 mg, 1.875 mmol). The reaction mixture was stirred at 70° C. for 1 h. Solvents were evaporated and the residue was purified by RP HPLC (MeCN and 0.1% HCOOH in water) to give 4e (two isomers, 108 mg, 30.2%) as a white solid. ¹H NMR (CD₃OD, 400 MHz) δ7.77, 7.85 (2d, J=8.0 Hz, 1H), 7.18-7.36 (m, 5H), 6.09, 6.12 (2s, 1H), 5.54, 5.63 (2d, J=8.0 Hz, 1H), 4.94-5.01 (m, 1H), 4.49-4.53 (m, 1H), 4.26-4.39 (m, 1H), 4.03-4.13 (m, 2H), 3.77-3.81 (m, 1H), 3.47 (s, 3H), 1.32, 1.36 (2d, J=7.2 Hz, 3H), 1.18-1.24 (m, 6H); ³¹P NMR (CD₃OD, 162 MHz) δ68.2, 67.7; ESI-MS: m/z 558.2 [M+H]⁺.

Example 38

The structures of compounds 3a through 3vv and 4a through 4f are shown in Table 9.

TABLE 9 ³¹P NMR Compound Product (solvent) MS

3a 67.12 67.86 (CDCl₃) 564.5 (M − H⁻)

3b 67.16 67.71 (CDCl₃) 543.2 (M − H⁻)

3c 67.05 68.08 (CDCl₃) 545.8 (MH⁺)

3d 67.89 67.96 (DMSO) 586.2 (MH⁺)

3e 66.9 66.9 (CD₃OD) 574.2 (MH⁺)

3f 67.85 67.16 570.4 (MH⁺)

3g 67.80 67.16 582.5 (MH⁺)

3h 67.92 67.28 592.2 (MH⁺)

3i 67.74 67.43 632.5 (MH⁺)

3j 68.01 67.35 620.8 (MH⁺)

3l 68.42 68.21 546.1 (MH⁺)

3m 69.17 68.68 558.1 (MH⁺)

3n 70.38 69.13 572 (MH⁺)

3o 69.15 68.56 586 (MH⁺)

3p 68.27 67.85 611.3 (MH⁺)

3q 68.09 68.03 613.7 (MH⁺)

3r 68.23 67.64 583.4 (MH⁺)

3s 68.07 67.71 623.1 (MH⁺)

3t 68.21 67.82 599.4 (MH⁺)

3u 68.21 67.65 597.5 (MH⁺)

3v 68.52 68.27 625.3 (MH⁺)

3w 68.43 68.32 637.6 (MH⁺)

3x 68.55 68.57 675.3 (MH⁺)

3y 68.66 68.36 687.4 (MH⁺)

3z 68.53 68.38 622.2 (MH⁺)

3aa 68.19 67.90 589.1 (MH⁺)

3bb 68.51 68.40 622.1 (MH⁺)

3cc 68.66 68.53 601.1 (MH⁺)

3dd 68.15 67.74 595.0 (MH⁺)

3ee 68.49 67.46 617.1 (MH⁺)

3ff 67.78 66.86 569.4 (M − 1)⁻

3gg 68.11 67.06 597.5 (M − 1)⁻

3hh 68.40 67.43 595.1 (MH⁺)

3ii 69.30 69.09 562.2 (MH⁺)

3jj 68.92 68.58 578.0 (MH⁺)

3kk 68.45 68.16 578.1 (MH⁺)

3ll 69.69 69.28 618.0 (M + Na)⁺

3mm 68.60 68.42 558.0 (MH⁺)

3nn 68.25 67.79 558.2 (MH⁺)

3oo 69.25 69.12 574.0 (MH⁺)

3pp 69.52 68.53 595.0 (MH⁺)

3qq 70.03 69.56 545.1 (MH⁺)

3rr 68.87 68.76 626.2 (M + Na)⁺

3ss 70.83 69.38 530.0 (MH⁺)

3tt 69.12 68.45 558.0 (MH⁺)

3uu 69.14 68.46 572.0 (MH⁺)

3vv 68.74 66.82 620.0 (MH⁺)

4a 67.71 67.74 (CDCl₃) 654.5 (M − H⁻)

4b 67.72 67.54 598.3 (MH⁺)

4c 68.44 68.42 682.4 (MH⁺)

4d 68.90 68.23 585.9 (MH⁺)

4e 68.2  67.7  558.2 (MH⁺)

4f 68.93 67.96 612.4 (MH⁺)

Example 39 General Synthesis of nucleoside 5′-O-(1-thiotriphosphates)

1,2,4-Triazole (42 mg, 0.6 mmol) was suspended 1 mL of dry CH₃CN. Triethylamine was added (0.088 mL, 0.63 mmol), and the mixture was vortexed to obtain a clear solution. After addition of PSCl₃ (0.01 mL, 0.1 mmol), the mixture was vortexed and left for 20 minutes. The mixture was then centrifugated. The supernatant was added to the nucleoside (0.05 mmol), and the mixture was kept at ambient temperature for 1 hour. Tris(tetrabutylammonium) hydrogen pyrophosphate (180 mg, 0.2 mmol) was added. The mixture was then kept for 2 hours at RT. The reaction was cooled in an ice-water bath and quenched with water. The 5′-triphosphate, as mixture of diastereomers, was isolated by IE chromatography on an AKTA Explorer using column HiLoad 16/10 with Q Sepharose High Performance. The separation was done using a linear gradient of NaCl from 0 to 1N in 50 mM TRIS-buffer (pH7.5). The fractions containing the nucleotide α-thiotriphosphate were combined, concentrated and desalted by RP HPLC on the same column as in Example 3. A linear gradient of methanol from 0 to 30% in 50 mM triethylammonium buffer was used for elution over 20 minutes, flow 10 mL/min. Two separate compounds corresponding to individual diastereomers at the phosphorus chiral center were collected. Analytical RP HPLS was done in 50 mM triethylammonium acetate buffer, pH 7.5, containing linear gradient of acetonitrile from 0% to 25% in 7 minutes on a Synergy 4 micron Hydro-RP column (Phenominex). Retention time (R.T.) for the individual diastereomers is provided in Table 10.

TABLE 10 α-Thiotriphosphates ³¹P ³¹P ³¹P NMR NMR NMR R.T. Structure Pα Pβ Pγ MS min

5b 43.17 d −21.69 m −5.32 d  513.0 4.17

5a 42.89 d −21.75 q −5.28 d  513.0 4.50

5c 43.14 d −23.80 m −10.20 bs 515.0 4.90

5d 42.12 d −23.48 q −6.49 d  515.0 5.52

5e 43.42 d −21.93 q −5.47 d  554.3 5.39

5f 43.07 d −21.90 q −5.40 d  554.2 5.79

5g 43.41 d −23.26 m −10.10 bs 552.2 5.23

5h 43.12 d −24.20 m −11.05 d 552.2 5.82 R.T. = retention time

In Table 10, 5a and 5b are diastereomers, and distinguishable by the chirality of the alpha-thiophosphate. Likewise, 5b and 5c; 5d and 5e; and 5f and 5h, respectively, are diastereomers and distinguishable by the chirality of the alpha-thiophosphate.

Example 40 HCV Replicon Assay Cells

Huh-7 cells containing the self-replicating, subgenomic HCV replicon with a stable luciferase (LUC) reporter were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 2 mM L-glutamine and supplemented with 10% heat-inactivated fetal bovine serum (FBS), 1% penicillin-streptomyocin, 1% nonessential amino acids, and 0.5 mg/mL G418.

Determination of Anti-HCV Activity

Determination of 50% inhibitory concentration (EC₅₀) of compounds in HCV replicon cells were performed by the following procedure. On the first day, 5,000 HCV replicon cells were plated per well in a 96-well plate. On the following day, test compounds were solubilized in 100% DMSO to 100× the desired final testing concentration. Each compound was then serially diluted (1:3) up to 9 different concentrations. Compounds in 100% DMSO are reduced to 10% DMSO by diluting 1:10 in cell culture media. The compounds were diluted to 10% DMSO with cell culture media, which were used to dose the HCV replicon cells in 96-well format. The final DMSO concentration was 1%. The HCV replicon cells were incubated at 37° C. for 72 hours. At 72 hours, cells were processed when the cells are still subconfluent. Compounds that reduce the LUC signal are determined by Bright-Glo Luciferase Assay (Promega, Madison, Wis.). Percent Inhibition was determined for each compound concentration in relation to the control cells (untreated HCV replicon) to calculate the EC₅₀.

Compounds of Formula (I) are active in the replicon assay. The antiviral activity of exemplary compounds is shown in Table 11, where ‘A’ indicates an EC₅₀<1 μM, ‘B’ indicates an EC₅₀<10 μM, and ‘C’ indicates an EC₅₀<100 μM.

TABLE 11 Compound EC₅₀

A

B

A

A

A

A

A

A

A

A

A

A

A

C

B

A

A

A

A

A

A

A

A

A

A

A

A

A

A

A

A

C

C

A

A

A

A

A

A

A

A

A

B

B

A

A

B

A

A

A

C

A

A

A

A

A

Example 41 NS5B Inhibition Assay

The enzyme activity of NS5B570-Con1 (Delta-21) was measured as an incorporation of tritiated NMP into acid-insoluble RNA products. The complementary IRES (cIRES) RNA sequence was used as a template, corresponding to 377 nucleotides from the 3′-end of HCV (−) strand RNA of the Con-1 strain, with a base content of 21% Ade, 23% Ura, 28% Cyt, and 28% Gua. The cIRES RNA was transcribed in vitro using a T7 transcription kit (Ambion, Inc.) and purified using the Qiagen RNeasy maxi kit. HCV polymerase reactions contained 50 nM NS5B570-Con1, 50 nM cIRES RNA, about 0.5 μCi tritiated NTP, 1 μM of competing cold NTP, 20 mM NaCl, 40 mM Tris-HCl (pH 8.0), 4 mM dithiothreitol, and 4 mM MgCl₂. Standard reactions were incubated for 2 hours at 37° C., in the presence of increasing concentration of inhibitor. At the end of the reaction, RNA was precipitated with 10% TCA, and acid-insoluble RNA products were filtered on a size exclusion 96-well plate. After washing of the plate, scintillation liquid was added and radio labeled RNA products were detected according to standard procedures with a Trilux Topcount scintillation counter. The compound concentration at which the enzyme-catalyzed rate was reduced by 50% (IC₅₀) was calculated by fitting the data to a non-linear regression (sigmoidal). The IC₅₀ values were derived from the mean of several independent experiments and are shown in Table 12. Compounds of Formula (I) showed activity in this assay. A value of ‘A’ in the table below indicates an IC₅₀ of <1 μM, a value of ‘B’ indicates an IC₅₀<10 μM, and a value of ‘C’ indicates an IC₅₀ value of <100 μM.

TABLE 12 IC₅₀ Structure value 5a

C 5b

A 5c

B 5d

C 5e

A 5f

A 5g

A 5h

B

Example 42 Hepatocyte Activation Assay

Plated human hepatocytes were purchased from CellzDirect. 30 μL of test article (compound 3a) in DMSO at 5 mM was dosed to the incubation medium (3 mL) of each well containing ˜1.5 million human hepatocytes to reach a final concentration of 50 uM. After 6 hours of incubation at 37° C., the medium was removed and the cells were washed twice with 500 μL cold 0.9% NaCl in H₂O. An aliquot of 500 μL cold methanol/H₂O (70/30) was added to the well to lyse the hepatocytes. The cells were scraped off the well, and the entire content was removed to an Eppendorf tube. After more than 3 hours of storing at −20° C., the lysate was warmed to RT, vortexed, and centrifuged. The supernatant was evaporated in a Speed-Vac, and the sample was reconstituted with 500 μL 1 mM ammonium phosphate in H₂O. 20 μL was injected into the LC/MS/MS system for the specific detection of the α-thiotriphosphate of the test article (see FIG. 1, panel D). A Thermo HyPurity C18 column (50×2.1 mm, 3u particle size) was used to achieve HPLC separation. Mobile phase A consisted of 3 mM ammonium formate and 10 mM dimethyl-hexylamine in H₂O and mobile phase B consisted of 3 mM ammonium formate and 10 mM dimethyl-hexylamine in acetonitrile/H₂O (50/50). The HPLC elution was via a linear gradient on increased mobile phase B at a flow rate of 0.22 mL/min. Compounds 5a and 5b were detected by a Sciex API 3200 via a negative ion MRM mode.

In FIG. 1, Panels A, B, C and D show the following. Panel A. HPLC chromatogram of a synthetic sample of the α-thiotriphosphate, 5a, at 300 nM in 1 mM ammonium phosphate in H₂O. Panel B. HPLC chromatogram of a synthetic sample the α-thiotriphosphate, 5b, at 300 nM in 1 mM ammonium phosphate in H₂O. Panel C. HPLC chromatogram of a purposely prepared 1:1 mixture of a synthetic sample of the α-thiotriphosphate diastereomers 5a and 5b, each at 150 nM in 1 mM ammonium phosphate in H₂O. This shows that compounds 5a and 5b can be distinguished. Panel D. HPLC chromatogram of the α-thiotriphosphate diastereomer formed following incubation of compound 3a in human hepatocytes. As illustrated by Panel D, only compound 5b is formed.

Example 43 Combination of Compounds Combination Testing

Two or more test compounds were tested in combination with each other using an HCV genotype 1b HCV replicon harbored in Huh7 cells with a stable luciferase (LUC) reporter. Cells were cultured under standard conditions in Dulbecco's modified Eagle's medium (DMEM; Mediatech Inc, Herndon, Va.) containing 10% heat-inactivated fetal bovine serum (FBS; Mediatech Inc, Herndon, Va.) 2 mM L-glutamine, and nonessential amino acids (JRH Biosciences). HCV replicon cells were plated in a 96-well plate at a density of 10⁴ cells per well in DMEM with 10% FBS. On the following day, the culture medium was replaced with DMEM containing either no compound as a control, the test compounds serially diluted in the presence of 2% FBS and 0.5% DMSO, or a combination of compound 3b with one or more test compounds serially diluted in the presence of 2% FBS and 0.5% DMSO. The cells were incubated with no compound as a control, with the test compounds, or the combination of compounds for 72 h. The direct effects of the combination of the test compounds were examined using a luciferase (LUC) based reporter as determined by the Bright-Glo Luciferase Assay (Promega, Madison, Wis.). Dose-response curves were determined for individual compounds and fixed ratio combinations of two or more test compounds.

The effects of test compound combinations were evaluated by two separate methods. In the Loewe additivity model, the experimental replicon data was analyzed by using CalcuSyn (Biosoft, Ferguson, Mo.), a computer program based on the method of Chou and Talalay. The program uses the experimental data to calculate a combination index (CI) value for each experimental combination tested. A CI value of <1 indicates a synergistic effect, a CI value of 1 indicates an additive effect, and a CI value of >1 indicates an antagonistic effect.

The second method utilized for evaluating combination effects used a program called MacSynergy II. MacSynergy II software was kindly provided by Dr. M. Prichard (University of Michigan). The Prichard Model allows for a three-dimensional examination of drug interactions and a calculation of the synergy volume (units: μM² %) generated from running the replicon assay using a checkerboard combination of two or more inhibitors. The volumes of synergy (positive volumes) or antagonism (negative volumes) represent the relative quantity of synergism or antagonism per change in the concentrations of the two drugs. Synergy and antagonism volumes are defined based on the Bliss independence model. In this model, synergy volumes of less than −25 indicate antagonistic interactions, volumes in the −25-25 range indicate additive behavior, volumes in the 25-100 range indicate synergistic behavior and volumes >100 indicate strong synergistic behavior. Determination of in vitro additive, synergistic and strongly synergistic behavior for combinations of compounds can be of utility in predicting therapeutic benefits for administering the combinations of compounds in vivo to infected patients.

The CI and synergy volume results for the combinations are provided in Table 13.

TABLE 13 Combination Synergy Volume Compound CI at EC₅₀ (μM² %) INX-189 0.42 65 PSI-938 0.73 27 PSI-6130 0.78 15 PSI-7851 1.1 0 GS-9190 0.92 79 Filibuvir 0.85 23 ANA-598 0.02 161 7008 0.01 127 VX-222 0.67 38 VX-950 0.06 76 ITMN-191 0.28 126 TMC-435 0.5 126 BMS-790052 0.64 26 Ribavirin 1 22 Pegylated 0.33 117 Interferon Consensus 1 31 Interferon Cyclosporin A 0.07 60 BILN-2061 0.7 31 HCV-796 0.42 31 IFN-Lambda 1 0.35 116 IFN-Lambda 2 0.49 34 IFN-Lambda 3 0.63 35

Furthermore, although the foregoing has been described in some detail by way of illustrations and examples for purposes of clarity and understanding, it will be understood by those of skill in the art that numerous and various modifications can be made without departing from the spirit of the present disclosure. Therefore, it should be clearly understood that the forms disclosed herein are illustrative only and are not intended to limit the scope of the present disclosure, but rather to also cover all modification and alternatives coming with the true scope and spirit of the invention. 

What is claimed is:
 1. A compound of Formula (I) or a pharmaceutically acceptable salt thereof:

wherein: B¹ is an optionally substituted pyrimidine base; R¹ is an optionally substituted N-linked α-amino acid or an optionally substituted N-linked α-amino acid ester derivative; R² is selected from the group consisting of an optionally substituted aryl and an optionally substituted monocyclic heteroaryl; R^(3a) and R^(3b) are both hydrogen; R⁴ is hydrogen; R⁵ is hydrogen; R⁶ is selected from the group consisting of hydrogen, —OR¹² and —OC(═O)R¹³; R⁷ is selected from the group consisting of hydrogen, —OR¹⁴ and —OC(═O)R¹⁵; or R⁶ and R⁷ are both oxygen atoms and linked together by a carbonyl group; R⁸ is selected from the group consisting of azido, cyano, halogen, and unsubstituted C₁-C₆ alkyl; R⁹ is hydrogen; R¹² and R¹⁴ are selected from the group consisting of hydrogen or an unsubstituted C₁₋₆ alkyl; R¹³ and R¹⁵ are selected from the group consisting of an unsubstituted C₁₋₆ alkyl or an unsubstituted C₃₋₆ cycloalkyl; and wherein when a substituent is substituted, the substituent is substituted with a group individually and independently selected from C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₃₋₈ cycloalkyl, cycloalkenyl, C₆-C₁₀ aryl, 4 to 14 atom heteroaryl, 3 to 18 atom heteroalicyclyl, (aryl)C₁₋₄ alkyl, (heteroaryl)C₁₋₄ alkyl, (heteroalicyclyl) C₁₋₄ alkyl, hydroxy, alkoxy, aryloxy, acyl, cyano, halogen, O-carbamyl, N-carbamyl, N-thiocarbamyl, C-amido, N-amido, S-sulfonamido, N-sulfonamido, C-carboxy, O-carboxy, nitro, sulfonyl, haloalkyl, haloalkoxy, an amino, a mono-substituted amino group and a di-substituted amino group.
 2. The compound of claim 1, wherein R² is optionally substituted aryl.
 3. The compound of claim 2, wherein R² is optionally substituted phenyl.
 4. The compound of claim 3, wherein R² is unsubstituted phenyl.
 5. The compound of claim 4, wherein R¹ is an optionally substituted N-linked α-amino acid.
 6. The compound of claim 5, wherein R¹ is selected from the group consisting of N-alaninyl, N-asparaginyl, N-aspartatyl, N-cysteinyl, N-glutamatyl, N-glutaminyl, N-glycinyl, N-prolinyl, N-serinyl, N-tyrosinyl, N-argininyl, N-histidinyl, N-isoleucinyl, N-leucinyl, N-lysinyl, N-methioninyl, N-phenylalaninyl, N-threoninyl, N-tryptophanyl, and N-valinyl.
 7. The compound of claim 4, wherein R¹ is an optionally substituted N-linked α-amino acid ester derivative.
 8. The compound of claim 7, wherein R¹ is an N-linked α-amino acid ester selected from the group consisting of N-alaninyl ester, N-asparaginyl ester, N-aspartatyl ester, N-cysteinyl ester, N-glutamatyl ester, N-glutaminyl ester, N-glycinyl ester, N-prolinyl ester, N-serinyl ester, N-tyrosinyl ester, N-argininyl ester, N-histidinyl ester, N-isoleucinyl ester, N-leucinyl ester, N-lysinyl ester, N-methioninyl ester, N-phenylalaninyl ester, N-threoninyl ester, N-tryptophanyl ester, and N-valinyl ester.
 9. The compound of claim 8, wherein R¹ is an N-linked α-amino acid ester, wherein the ester is selected from the group consisting of isopropyl ester, cyclopropyl ester, isobutyl ester, cyclobutyl ester, neopentyl ester, cyclopentyl ester, and cyclohexyl ester.
 10. The compound of claim 9, wherein R¹ is selected from the group consisting of N-alaninyl isopropyl ester, N-alaninyl cyclohexyl ester, N-alaninyl neopentyl ester, N-valinyl isopropyl ester, and N-leucinyl isopropyl ester.
 11. The compound of claim 10, wherein R¹ is N-alaninyl isopropyl ester.
 12. The compound of claim 1, wherein R⁶ and R⁷ are independently selected from the group consisting of —OH and —OC(═O)R¹³; or R⁶ and R⁷ are both oxygen atoms and linked together by a carbonyl group.
 13. The compound of claim 12, wherein R⁶ and R⁷ are both —OH.
 14. The compound of claim 13, wherein R⁸ is unsubstituted C₁-C₆ alkyl.
 15. The compound of claim 14, wherein R⁸ is methyl.
 16. The compound of claim 1, wherein B¹ is an unsubstituted pyrimidine base.
 17. The compound of claim 16, wherein B¹ is


18. A compound of Formula (I), or a 5′-thio-monophosphate thereof, or a pharmaceutically acceptable salt of the foregoing:

wherein: B¹ is an optionally substituted pyrimidine base; R¹ is O⁻ or OH; R² is

 wherein R¹⁹, R²⁰ and R²¹ are independently absent or hydrogen, and n is 0 or 1; R^(3a) and R^(3b) are both hydrogen; R⁴ is hydrogen; R⁵ is hydrogen; R⁶ is selected from the group consisting of —OR¹² and —OC(═O)R¹³; R⁷ is selected from the group consisting of —OR¹⁴ and —OC(═O)R¹⁵; or R⁶ and R⁷ are both oxygen atoms and linked together by a carbonyl group; R⁸ is selected from the group consisting of azido, cyano, halogen, and unsubstituted C₁-C₆ alkyl; R⁹ is hydrogen; R⁸ is selected from the group consisting of halogen and unsubstituted C₁-C₆ alkyl; R⁹ is hydrogen; R¹² and R¹⁴ are independently hydrogen or an unsubstituted C₁₋₆ alkyl; and R¹³ and R¹⁵ are independently an unsubstituted C₁₋₆ alkyl or an unsubstituted C₃₋₆ cycloalkyl; and wherein when a substituent is substituted, the substituent is substituted with a group individually and independently selected from C₁₋₆ alkyl, C₂₋₆ alkenyl, C₁₋₆ alkynyl, C₃₋₈ cycloalkyl, cycloalkenyl, C₆-C₁₀ aryl, 4 to 14 atom heteroaryl, 3 to 18 atom heteroalicyclyl, (aryl)C₁₋₄ alkyl, (heteroaryl)C₁₋₄ alkyl, (heteroalicyclyl) C₁₋₄ alkyl, hydroxy, alkoxy, aryloxy, acyl, cyano, halogen, O-carbamyl, N-carbamyl, N-thiocarbamyl, C-amido, N-amido, S-sulfonamido, N-sulfonamido, C-carboxy, O-carboxy, nitro, sulfonyl, haloalkyl, haloalkoxy, an amino, a mono-substituted amino group and a di-substituted amino group.
 19. The compound of claim 18, wherein n is
 1. 20. The compound of claim 19, wherein R⁶ and R⁷ are independently selected from the group consisting of —OH and —OC(═O)R¹³; or R⁶ and R⁷ are both oxygen atoms and linked together by a carbonyl group.
 21. The compound of claim 20, wherein R⁶ and R⁷ are both —OH.
 22. The compound of claim 21, wherein R⁸ is unsubstituted C₁-C₆ alkyl.
 23. The compound of claim 22, wherein R⁸ is methyl.
 24. The compound of claim 18, wherein B¹ is an unsubstituted pyrimidine base.
 25. The compound of claim 24, wherein B¹ is


26. A pharmaceutical composition comprising a therapeutically effective amount of a compound of Formula (I) of claim 1, or a pharmaceutically acceptable salt thereof, and a pharmaceutically acceptable carrier, diluent, excipient or combination thereof.
 27. The pharmaceutical composition of claim 26, wherein the compound of Formula (I) is

or a pharmaceutically acceptable salt thereof.
 28. The pharmaceutical composition of claim 27, wherein the composition is formulated for oral administration or intravenous administration.
 29. A method for ameliorating or treating a HCV infection comprising contacting a cell infected with the HCV virus with an effective amount of a compound of Formula (I) of claim 1, or a pharmaceutically acceptable salt thereof.
 30. The method of claim 29, wherein the compound of Formula (I) is

or a pharmaceutically acceptable salt thereof.
 31. The method of claim 30, further comprising contacting the cell with a second therapeutic agent, wherein the second therapeutic agent is selected from the group consisting of pegylated interferon-alpha-2a, pegylated interferon-alpha-2b, interferon lambda 1, interferon lambda 2, interferon lambda 3, consensus interferon, ribavirin, cyclosporine A,

or a pharmaceutically acceptable salt of any of the aforementioned compounds. 